So, I haven't played the game but, just from looking at the 3 disputed trophies,
Impossible Boy - says "Beat Cotton Alley dark world without dying"
switch satisfies The Real End - "You completed the Dark World..."
and if these are the last things to complete to get 1OO% it would satisfy I'm A Golden God! - "got a 1OO%"
and then the plat right after.
But without playing the game, doesn't seem far fetched
I just don't know how the levels link or whatever
But as far as the order in which the popped, I've had games that pop them out of order when they're all popped together.
Kinda like when you auto sync Shape Sounds on a different system after get that first plat or 1OO%.