Hi Sagefigaro,
I've never experienced these bugs and never saw them when other people used that tool (there has been a few randomizer speedruns). There's a guy who experiences soft-locks during some black screen transitions between fields, but I've always assumed that it was a bug from the emulator because this tool really doesn't modify the fields at all.
By any chance, maybe you are not using the US version of the game? That's the best explanation I've got for your bugs. The tool only checks for the file size but maybe it could misread another version and confuse it with the US version if they have the same file size (which would explain those bugs). Or maybe you applied another hack before? Though I don't know any hack for the PSX version that would shift the datas like this...
I am not really planning to work on that tool anymore. At some point, I would like to include it inside my other tool, Hades Workshop, to make it compatible with the Steam version of the game other among things. I didn't understand your suggestion to "randomize characters"? You mean replace every characters and non-playable characters with another one on the fields? That would be insane ^^'
But no, it would be way too much work (as you say, there's the problem with animations that has no convenient solution) only for cosmetic changes (even if I don't underestimate their importance, it's not the kind of things you'd randomize IMO).