Hmm. That's true. I guess what stood out to me more were the scenes they kept in the movie that lacked weight. With how they handled what was included, I don't think adding scenes in would've fixed the core issue. Illya confronting Beatrice after their battle, Julian getting impaled by Saber's sword, Miyu using Gae Bolg on Sakura...these were all highly emotional scenes in the manga but we sped through them in the movie. Same goes for actual battle scenes as well. There was never any tension.
Nah. Not that we had too much time to focus in the manga, the movie just speed-runs through events (and outright cuts certain scenes due to said speed-running).
Spoiler:
Yeah. I'd definitely have loved if they kept those scenes in, but the reason those opening scenes are still the highlight for me is simply the pacing. There's time spent on Illya getting up and looking outside, so those simple actions feel more meaningful than most other scenes; and again, that really shouldn't be the case with how many climactic moments are included.
I think it could still work. One of the fairies Darius and Pandora were seeing all along was Illya to begin with, so having her role with that box go further would be natural enough.
There are other options of course. The box could contain power left by the Old Gods which may be all Pandora needs to restore her functions as a "key" in the modern era. Illya may not be traveling with Pandora at the moment and bringing Illya back to the modern era could be a feat that everyone works together to accomplish.
Illya certainly doesn't need to be in the box or the only thing in the box.