I'm with you. Stuart Houston's theory seems to rely on Gilroy driving around aimlessly, or at best paralysed by indecision. If he didn't take any tools with him to accomplish some sort of burial then he was planning on just dumping her all along. This would have been very unwise for the reasons stated - as graphically demonstrated by the later conviction of Flynn in very similar circumstances. I do not think Gilroy was unwise in that respect. However, if he did intend to dump the body with minimal concealment, the sensible plan would be to drive as quickly as he reasonably could and spend as little time as possible offloading the body, so as to leave no opening for the police to say, this is suspicious, what were you doing all this time? It's a very long way from Edinburgh to Lochgilphead and there are actually three reasonable routes (including the M8 one). If he left no clue which way he'd gone (just don't turn the phone on at all, or even better, accidentally leave it behind) or at what point he'd stopped, it would have been a hopeless search. The missing hours, to me, point inexorably to an intent, and an attempt, to conceal the body.
The misdirection could well have been part of such a plan - drive the northern route, leave phone clues to suggest he drove the southern route, but dump her somewhere on the northern route. But the huge amount of missing time still argues against this.
Also, as you say, if he only thought to dump the body somewhere, he'd have done it much sooner. I've driven up Strathyre and Glen Ogle. It's crawling with promising places. If he was disorganised and panicking a bit, he'd have spent a lot longer on that leg as he investigated one possibility after another, maybe driving up to Balquhidder, or the south Loch Earn road, or up towards Loch Tay. But he drove without significant delay all the way to Tyndrum. At least.
So we have someone who has decided to dump the body, not bury it (by the police theory). He isn't equipped to bury a body, and he isn't going to try. But he has decided on (say) Glen Croe as the dumping place. So he drives this insane detour through Tyndrum to sneak up on Glen Croe from behind - even though driving the straight road through Glen Croe was his usual route and the route police would probably assume he would take anyway. Once there he becomes so paralysed by indecision that he drives around at speed for over an hour, clocking up the miles in a way that could only be done on the A roads, but somehow identifies a dumping spot in the course of this - but then doesn't dump the body but goes on to Lochgilphead with it. He realises then that the cops want to talk to him ASAP, but he still doesn't hurry, wasting another half hour before he sets off back, then goes back to his chosen spot - but again he drives around at speed clocking up more unnecessary miles on the A roads before (or after) just offloading the body. Then instead of going straight back via Tarbet he sets off again on that mad pointless northern loop, only to turn south in Crianlarich and go through Tarbet anyway.
I know the cops brought in a psychologist to try to figure out what he would have done, but I'm buggered if I know how any psychologist would have come up with that one.
You are absolutely right about the logic of taking the body to the school in his car - and why wouldn't he, he took it to the Chinese restaurant the previous evening with the wife and kids in the car. He's nothing if not bold. The best plan would have been to drive straight to Lochgilphead, and leave no missing time during which he could possibly have got rid of a body. Then on the way back go to his chosen disposal site, and he has a substantial chunk of time to play with. It's going to be a lot easier to dream up a reason for a delay on the way back only, and especially as he doesn't have any special reason that he knows about to get back in a hurry. He could have gone into the R&BT area, spent as much as four hours there, then maybe done the misdirection thing up through Tyndrum with his phone on to mislead the cops into thinking the body was up in Glen Orchy or thereabouts too. But he didn't do that either.
I think the missing time in the afternoon suggests incontrovertibly that he meant to get rid of the body on the outward journey. Why he chose to do that rather than go directly and do the disposal on the way back I don't know, but that's what he decided. I think he knew when he set off where he was going, otherwise he wouldn't have driven straight to Tyndrum. Organised killer, as you say. I think the job took longer than he anticipated (I don't seriously think he would have gone back to the same place only to dispose of other things from his car if he was satisfied he'd concealed the body) and had to leave it and go on to Lochgilphead. I do not think that the time was lost in searching for a disposal site, he already knew where he was going, but getting a body out of a car and buried or very well concealed is not a quick job, especially if you're getting changed to ensure that you're forensically clean.
The call to his office might have been mistake no 2. However I imagine he wanted to make contact with them while he was at the school to establish that he was indeed in Lochgilphead and there was nothing furtive about his journey. Had he even seen that there were voicemail messages on his phone that had been sent during the time it was off? He probably got a bit of a fright when he found himself talking to a cop, but he kept his head and at that point nobody really suspected anything. But that call meant that he didn't have an open-ended window on the way back, as he'd promised to go straight to Corstorphine. (It did, however, mean that he had a heads-up that he needed to get that car and himself as forensically clean as possible before he got to Edinburgh, so that was a plus.)
I think he went back to finish the job, and dispose of anything incriminating in his car at the same time. I don't think the disposal site was far from his core route, because he couldn't afford for his car to be seen in a place incompatible with a blameless drive to Lochgilphead and back. I don't think he drove around for an extra couple of hours just to waste time and burn diesel either. I think he did drive around to try to mislead the police, but that exercise is part of his known journey - taking the Tyndrum route instead of the R&BT, then ducking down through Ardlui to make it look as if he'd taken the R&BT route all along, and leaving strategic phone traces.
I can't see any other explanation for all of this other than that he knew of somewhere between Tyndrum and Inveraray where he intended to conceal the body. He turned his phone off at Nyadd and back on in Inveraray so that the police couldn't tell which of the two routes he'd taken. He went to his chosen spot but he but underestimated the time necessary to complete the job. He got dressed again leaving the job unfinished and went to the school - still later than he'd have liked to have been there. (I now seriously think that was his first serious mistake, he should have gone straight there, but I can see why he might not have thought that one through.) While there he discovers that the police want to talk to him, and he has to go to Corstorphine. As a witness there's no reason he should have imagined they might want to look at his car, but he told Darell Brown that he wanted the bin bags to tidy his car because he didn't want the police to see it untidy. Go figure! (I have been to police stations to talk to the police as a witness and it never occurred to me that they'd want to inspect my messy car!) He now has more to do than he perhaps anticipated, because he and the car have to be forensically clean that night. So back to the disposal site, finish the job, and get rid of everything in the car used to transport the body, dig or otherwise conceal it, and any protective clothing.
I think it's possible that his original intention might have been to drive straight back over the R&BT without stopping, leaving a trace, and let the cops imagine he'd gone that way both ways. But he can't do that, he has to go back up to the disposal site around Dalmally/Tyndrum. So at some time during his journey (he had a lot of driving time to think) he hatches the plan to duck down the A82 at Crianlarich to make it look as if he'd come over the R&BT, by means of phone manipulation. And this I think was mistake number 3, he turned the phone on about five minutes too early. (Calling it #3 is probably being over-critical; the phone call to the office was arguably not a mistake, or if it was, it's not something he could reasonably have anticipated.)
Nothing else makes a blind bit of sense. I wish so much I knew what other evidence the police are relying on that makes them reject this. I wish I knew what they imagined he was thinking when he did all the bizarre and pointless driving they believe he did. And I wish I knew why they don't think these very precise (with one slip-up on the last one, when he was tired and perhaps disoriented) phone on/off switches were supposed to achieve.
Also, why, if his plan was to drive the Tyndrum route to draw the investigation up that way and away from the R&BT, did he so carefully manipulate the phone pings so as to leave no trace at all that he went that way? There's no way he knew he was going to get caught by that camera at the Green Welly.
I've said all this a dozen times. I just keep hoping I'll think of something else that points in a different direction we can explore as something new. I keep hoping I'll think of a way that the police theory makes sense. But I can't. I'm going to bed.