No, not a mess at all. If a schedule change after one has started traveling, or unforeseen circumstance (weather or mechanical issue, etc.) beyond the transit passenger's control causes the traveler to go over the 24- (or 48-) hour limit, the Chinese are reasonable about this, display a bit of common sense, and just extend the gratis period as needed to allow the circumstance to get resolved. Usually no extra or special paperwork is involved. Immigration is perfectly able to find out/corroborate airline schedule and aircraft issues, also airport-wide delays.