Thanks for the great tool!
I think, as a user, if you implemented that auto-save I would probably make multiple instances of the program, one for each environment component. That would get me where I'd like to be. I know putting arbitrary save/load conditions in is a nightmare, so if the autosave/load is low hanging fruit... well, that's probably the 80% solution. And a relatively easy 80% is miles better than an impossible 99%.