Multiple versions are fantastic as long as its cohesive and makes sense in the context of that universe... but I guess that's just an opinion. With Star Tours, I can see how others, who may not be "die hard" fans, wouldn't mind as much and would have a good time despite the lack of story not making sense. (not to assume your not a die hard SW fan )
It's not like I don't notice. I do. For me, part of the fun is wondering what scenes will come up. MF:SR would be much better if it had more randomized scenes.