I have obtanied the 1000000% trophy after buying the physical copy! As soon as I installed the game 3 (or 4 i don't remember exactly) secret appeared in the secret list and they were locked.
1 Secret was for "unlocking the greedier mode" which unlocks if you donate 500 coins to the greed machine, another one was for unlocking "Apollyon" (which i already unlocked in my previous game save of the digital version) which unlocks if you defeat megasatan, then there was another secret that unlocked the "Void" (that again i already unlocked in my digital game save) whick i think (but maybe i don't remember well) unlocks if you beat the Lamb , and maybe there was another one. (I'm not sure)
Anyway I am not a cheater, I won the trophy following the advice of another player here on this forum.
For some unkown reason the physical version of the game has theese extra secrets that the digital version don't have because it unlocks thoose secret in a different way (for example I remember that Apollyon was already available when i installed the update, and i didn't have to defeat megasatan to unlock him...). This could be the reason why the trophy doesn't pop up in the digital version since the game still needs the secret of the physical version...