Apparently the bug that breaks your characters, and effectively your game is known and reported, and it's caused by removing your originally created characters from the party at any point. This will not only break the "main" characters (ie, it will randomise their ability points and reset all skills to 0 without refunding any skill points as in the screenshots I posted above), but will also make other custom created characters in your roster to randomly appear and disappear from the roster manager.
This is a gamebreaking bug that completely ruins the playthrough for you if you didn't notice as it's also a bug that sometimes doesn't manifest immediately and by the time you notice, all your saves are already corrupted and the only known way to fix it currently is restarting the game from scratch, as I had to do.
So for now, restrain yourselves from benching your two original characters for any reason, be it to improve your party, use a weaponmod/armourmod char instead while you're in your base, etc. as it will break your game irreversibly.