I honestly have to wonder if that 40% quote was referring to file size, not something nebulous and hard to apply a percentage to like "content". And we all know that the biggest eaters of data on CD games in that era were things like redbook audio and FMV. It's very possible that we didn't lose much in terms of sprites, areas, and things that involve actual gameplay. Theoretically, we could've lost story told through FMV, but games of this kind back then always told the majority of their story with in-game text and sprites. A CD version of Secret of Mana may have been very similar, just a little flashier, like Sega CD versions of regular Genesis games.
It'd be great if somebody could dig up the source of the quote and those who understand Japanese could have another crack at it to see if anything's been lost in translation.