Update: WE HACKED* THE SCRIPTS
Trying to figure out how to modify treasure chest contents sent me down a month-long rabbit hole (which I would not have been able to work through without some very helpful people in the Baten Kaitos Discord server), but it's finally yielded some results.
All the treasure chests, quest magnus sources, interactable items, and more are controlled by a bunch of special scripts that were basically ripped straight from the gamecube version. By modifying the magnus ids that we find in these scripts, we can change the following:
Magnus found by searching places*
Quest magnus requirements (e.g. tree needs to be burned with Pow Milk instead of fire)
* Now there's one really big caveat with those treasure chests, at least for now: We can only change a magnus id to a magnus id with the same number of bytes. We can't change the total number of bytes in the script (yet) so for the time being we have to divide magnus into two groups:
One byte: Weapons, armor, yells, artifacts (earth sphere, etc.), escape, cameras, and voices
Two bytes: Spells, finishers, auras, class-ups, constellations, equips, camp items, healing items, all the random items (magic beans, sushi, etc.), photos, and quest magnus
(Or put another way, any magnus in the collection up to and including voice 6 is one byte, everything after that is two.
Oh yeah, and you'll also notice that while we can control what magnus you get, we haven't been able to figure out where it gets that text from. So you'll still see the name of the magnus that's suppoed to be there.
I honestly think this could still be fun in a randomizer, we'd just be switching weapons and armor with other weapons and armor and all the rest amongst all the rest.
But there's still the tedious job of finding all those scripts in the game files, extracting and decompressing them, and finding the exact location in the script of each of the magnus ids. Because of that, this won't be in the first release of the randomizer lol.