The engine may already do this, I'm not sure, but if not... in the future, might it be possible for save files to include a list of mods running when they are saved, and appear with warning if you have them in the list when loading other mods (or vanilla?) Maybe a line in the save description regarding 'These mods were running at the time'.
Not exactly an issue yet, but with mine coming as more of a full-conversion (and we know I won't be the only one, right?) it might get a little hard for people to eventually separate which saves are with which mods. And loading one without the proper mods may start to give all sorts of errors once you start considering custom equipment and skills.
Good idea, thank you.
Added to our todo list.