I think it's fine if there is limited compatibility between versions. ie: (not knowing the internal structures, but taking an educated random guess) You could have three groups: NotEye+ADOM Mac/PC/Linux, plain-ADOM DOS/Mac/Linux, and ADOM Amiga (and maybe Raspbian? ..all the old Big-Endian architectures.) ..I think the vast vast majority of players would be fine if you can only transfer games within the first two groups, and 'odd' ones like Amiga, Raspbian, and MacOS PPC games will only work on that platform.
My logic for this is that, I think, most players will be sticking religiously the NotEye or non-NotEye version these days. And for the odd ones: I do still play the Amiga port from time to time, and honestly I don't expect any special treatment. I'm still just pleased it gets supported at all. If I can't use that save on other platforms, that's fine. If there's limited compatibility, maybe it's just worth listing, to the right of the save-game, what platform it was created on. Then players can easily know if they can open it on the platform they're on, and the game will just refuse to load, say, the Amiga version, saying: "Sorry, the structure of saved-games is quite complex, and the Amiga version can't be opened on Windows."
Anyway, just my random ideas. I don't think the ADOM team needs to go to extraordinary lengths to get save-games transferable between absolutely every variant. ..then it's just code to update from the last one or two versions.