I play with a lot of mods, from those for construction to mods for graphics, but a lot of the time I also play in several sandboxes and maps and this becomes a problem when playing with mods because when I enter another game the mod is no longer necessary or sometimes not allowed, which forces me to disable the mod to play in that specific world. It would be interesting to see the possibility of having mods activated only for that world (sandbox) so I don't have to go through the hassle of activating and deactivating mods every time I change sandboxes, for example:
I enter a world saved in RSS and it has the RSS Rebalance mod, but when I go to play in the stock world I no longer need this mod since it hinders the performance of crafts in that system, which makes me have to disable the mod, restart the game and then be able to play without the mod in that world.
Hope you understand :)
having game mods be applicable per save file rather than globally would be quite nice (i myself can't benefit from it cause i'm on ios, but your example is a perfect reason why it'd be good to have)