If I remember correctly, Amanda and Raffaele both wrote about Meredith as having gone out without saying where she was going. There is no evidence, that Amanda and Raffaele gave any thought to Meredith's whereabouts that night.
If that's the case, then (as you point out) there's little reason to suppose that Knox should have been particularly expecting to find Meredith in the cottage on that Friday morning. As I've said before, that day was a public holiday with no university (although it appears that Meredith and her English friends may have forgotten this, though Knox had not).
My view is this: if Knox didn't notice the broken window and mess in Filomena's room on her entrance to the cottage that morning, then what she was looking at was an open front door, some small evidence of blood in the small bathroom, and unflushed faeces in the large bathroom. All of these would count as unusual and a little disconcerting, but certainly not indicative that anything criminal or injurious had occurred.
But when Knox discovered the situation in Filomena's room, suddenly the element of a break-in and possible burglary was introduced. Now there was some evidence of criminal activity, and the blood and faeces took on a different connotation. At this point, Knox would have wondered where Meredith and Filomena were (assuming she knew that Laura was away). And since she and Meredith were not only closer than her and Filomena, but also they were obviously able to communicate far more easily, it makes sense that Knox tried to reach Meredith.
When Knox tried and failed to reach Meredith's two mobile phones, I still think that there would have been no immediate reason for her to be especially worried about Meredith's welfare. She and Meredith led very separate lives, and Meredith might very well have been anywhere, doing anything (or sleeping). But I think that when Knox had not heard back from Meredith 15 minutes or so after her first attempts to reach her, this - coupled with trying her bedroom door and finding it locked - started to raise concerns. One other important factor here - which Knox was well aware of - is that Meredith generally kept her UK phone close at hand and switched on constantly, on account of her mother's medical condition. Knox would therefore have found it worrying that Meredith wasn't responding to calls to this phone.
So, personally, I find the escalation of concern on the morning/lunchtime of the 2nd November to be entirely plausible and non-contrived. There is (to me) a logical progression from the time Knox first walked through the door of the cottage to the fairly major concern about Meredith's welfare at the time her bedroom door was broken down.
OT: Watching Kool & the Gang's Glastonbury set on BBC4 right now

I was offered a nice ticket + accommodation package for Glasto, but declined on the grounds of work and mud. As it happens, I could have rejigged work commitments, but the mud this year was even worse than usual - so I'm quite glad to be watching it on TV. "Oh yes it's layyyyydies' night, and the feeeeeeling's right........."