You do not need to select a mod when loading a savegame. SE5 automatically loads the mod when you attempt to load the savegame.
The downside of this is, you're right, you can't change the mod being used in a savegame without actually modifying the contents of the mod data folder. This means that in order to upgrade a game to a newer version of a mod, the newer version must overwrite the older version, forcing everyone on PBW to upgrade their copy of the mod. I suppose it's something that we'll have to live with until Aaron implements a "mod override" in the UI or command line somewhere. But it really shouldn't be all that bad - it SHOULD mean less confusion when mods are upgraded, as all games will be upgraded simultaneously! And if the new version of the mod is incompatible with the old, well then it ought to get a new folder name!
Still, great work at getting SE5 supported! It came as a complete surprise!