As I've mentioned earlier, my experience isn't very helpful on the subject of multi-point residential locks, since they have only recently begun see much exposure in the U.S. Even that is diminished by the fact that the U.S. implementations have developed new features and design considerations to cater to the U.S. market which are only now starting to find their way back to Europe.
Notable among these differences are changes to the lever operation of the outer bolt points, and the behavior of the interior thumbturn/key cylinder. (I should perhaps point out, again, that the popularity and use of interior keyed deadbolts has fallen dramatically in the U.S. in past decades, largely because of quite legitimate and serious safety concerns for the occupants of a home with such a lock design.)
The general knowledge of the field that my experience has supplied suggests to me that any of these options are possible, and many are quite likely. There is nothing unusual about a lock with a key mechanism which operates both spring latch and deadbolt. There is also nothing unusual about a door equipped with a deadbolt which only operates from the inside. When put into use it requires anyone who desires entry to knock on the door and ask to be let in. Whether they live there or not. This is hardly uncommon.
Often this feature is known as a "night latch". Sometimes it is the result of multiple separate locksets having been installed (often implemented with the addition of a "rimbolt" or surface mounted deadbolt). Sometimes it can be part of a single implementation. In the case of multi-point locksets this would seem to be a quite logical feature to make available.
What I have read since this topic came up has led me to understand that the full gamut of application variants are generally available for multi-point locks (even more, at least now, in the U.S. than in Europe), just as they are for older style locksets.
One rather basic alternative of design options, available on both continents, is either "automatic" or semi-automatic". The latter requires a conscious action by the user to engage the outer bolt points. This is probably the lever action we have been discussing. The former automatically engages all three deadbolt points when the door is closed. Both can be implemented with a function which disengages both the deadbolts and spring latch using a key. So far I have been unable to uncover enough technical detail to determine how controllable the automatic function is by the user, or how it may be actuated.
I don't know if it is helpful to point this out or not, but the Corbin lockset which Dan O. and I both noticed as a remarkably likely candidate is in a price range which suggests that there would be very few standard features which were not available for it. The interchangeability of hardware elements within any given manufacturer's product line also means that a competent locksmith can often quite easily implement features which are not indicated in the standard catalog descriptions. The likelihood of this increases with the complexity of the lockset.
This gets us right back to the quandary of determining what features were available for that particular lock, and which of those available features were chosen to be implemented.
I do honestly recognise your expertise in this area, and the amount of research that both you and Dan_O have put in. Like you, I just think that there's incomplete information to make a definitive judgement here, however I still think that plenty of other things point towards the constant use of a key (and a key alone) to not only lock the door, but even to keep it firmly closed. Obviously the deliberately disabled latch is one of those factors, but, to me, the more important one is the testimony of all the girls in the house (excluding Meredith, unfortunately and unavoidably). There seems to be a singular agreement among them that keys were used to lock the door from both the inside and the outside, as a matter of course.
And this is why I think that whoever exited the door that night either found the door unlocked (either still shut, or blown/swung ajar), or needed a key to unlock it before leaving. Of these two options, I think that the latter is by some distance the most likely - regardless of which murder scenario one favours.
As I've said before, for what it's worth, I think that the following scenario is feasible and possible:
1) Guede broke-and-entered via Filomena's window at around 20.50, made a very cursory start on his search for money and small valuables (jewellery, small electronics items etc), then got a sudden urge to empty his bowels (driven in part by the well-documented link between heightened fear/adrenaline and bowel motion), and went to the large bathroom.
2) Meredith then arrived home at just before 21.00, locked the front door behind her using her key, perhaps went to the refrigerator and ate a piece of mushroom, then went to her room and started to call home to the UK.
3) As soon as Meredith went into her room, Guede seized his opportunity to emerge from the large bathroom - without flushing, so as not to alert Meredith to his presence. He went to exit from the front door, but found it locked and therefore a barrier to exit. He tried pulling on the door, and started hunting around the kitchen/lounge for keys.
4) Meredith heard a commotion, and terminated her call home before it was even answered, in order to investigate. She went to her bedroom door and looked out to the hallway, to be confronted by Guede. He then raised a knife and forced her back into her room.
5) The attack and murder, together with the sexual assault, then took place for reasons that are near impossible to correctly define. Perhaps Meredith refused to give Guede keys to the door. Perhaps she said that she was going to call the police, and made to use her phone. Perhaps Guede just snapped at this point. Maybe he penetrated her digitally while she was dying and he was in an adrenaline-fuelled sexual frenzy. Maybe he masturbated in front of her as she lay dying, depositing semen on the pillow. Either way, the upshot was that Meredith was dead or dying on her bedroom floor, and Guede was now a sexual murderer with blood on his hands and clothes.
6) Guede now realised that he had to leave the scene, and that he would have to clean himself off to a fair degree before leaving. He went to the small bathroom, and turned on the light, then removed one or both shoes in order to place his lower leg into the bidet or shower to remove blood from his trousers. At some point, he stood in a mixture of blood and water coming off from his bloody hands/clothing and pooling in the bottom of the bidet or shower, then stepped onto the bathmat - leaving a footprint in a blood/water mixture.
7) He returned to Meredith's bedroom (and maybe took one further trip to the small bathroom for the second towel), mopped up some of the blood, and moved her body fully onto the floor and on top of the pillow, stepping on the pillow various times in the process. He then went through Meredith's handbag to find her keys, and opportunistically took her rent money, credit cards and phones as well.
8) Guede got up from the bed (where he'd been going through the handbag), and stepped over Meredith's body in order to exit her room. As he did so, he stepped in some of her blood which was now pooling on the bedroom floor. He turned briefly on exiting to lock Meredith's bedroom door - to try to delay discovery by her housemates - and headed to the front door, leaving bloody footprints behind him.
9) Guede unlocked the front door and existed quickly when he saw that no cars or pedestrians were passing by. He didn't pause to lock the front door behind him - he merely pulled it shut, assuming perhaps that it would lock of its own accord.
Obviously, there are areas of this alternative narrative that are open to debate, and probably even open to attack. And I would welcome such debates or attacks - I'll either refine the narrative or abandon it if there are insurmountable problems with it. But bear in mind that if this narrative were put up to counter the prosecution's case, the defence wouldn't have to prove every element of it - they would merely have to show that each element was reasonable and possible. And that's all that I seek to achieve as well.