Except it really isn't a stretch -- the preshow video did a very good job setting up the attraction that way.
Sure Eisner wanted to push the thing into the parks, but they did the work and found the place where it fit. That's the way to do it - that's what makes it a Theme Park. You could say what you said for anything: "Yeah, the Seven Dwarfs Mine Train makes sense thematically where they put it, but knowing this new school WDI it could have been located somewhere else where the theme may not have made as much sense". It doesn't matter that they could have put it somewhere it didn't fit, they DID put it somewhere that it does. Like they should have with Guardians.
I'm not saying that I wish they'd put a 3D Guardians movie into the Magic Eye Theatre, but if they did I'd be less miffed about it. At least then the comparisons to Captain EO of a rag-tag band of Galactic Warriors with a funky, thumping soundtrack would have been fit under the same umbrella of the Imagination pavilion.