And again, to address really the whole issue, these kind of changes in location are done all the time, in lots of movies. Perhaps they were better disguised, and a discussion as to why they were noticeable in ROTF is a reasonable discussion to have I think. From my perspective, I think that Bay isn't as concerned with those kinds of dramatic changes as perhaps other directors are. Most people probably don't know that the boneyard isn't there, or that Karnac is nowhere near the Pyramids. But in the context of the story, I don't really think Bay sees it as important. He's not making a documentary. I think in this kind of "fantasy" film (and to some extent, almost all movies are fantasy), it's not critical whether or not the film "reality" matches up with the actual reality. He appears to pick locations (and consequently connects those locations in the film) based on their visual aesthetics and ability to be shot.
To be honest, there were a few things that bugged me as well. I think that overall, the last section of the movie was too short. I think that it suffered from a lack of exposition about what was happening and why it was happening.
For example, a scene after the decepticons arrived in Egypt showing multiple protoforms scanning the same vehicle would have completely solved the "problem" of Devestator and the constructicons being in the same place. I don't know if that was the actual reason for the "problem" but that's what I would have tried to do.
As another example, some scene or line of dialogue indicating where Megatron really is when we first meet the Fallen.
Or something that would have emphasized a little more that Sam's "destiny" was to save Optimus (as described in the Prime "heaven" scene). Something perhaps like a vision, dream, premonition, etc. earlier in the movie. Maybe as a part of the visions Sam has, he sees the Primes for a split second, and doesn't understand what it means.
Anyway, I actually like these discussions, I have to admit. It appeals to the very small part of me that is a writer/director/filmmaker trying to get out of my researcher/scientist mind.
And once again, I've been unable to stop myself from writing and writing and writing.