Given that we're able to check multiple mods in the Mod menu, I would think that it's a temporary thing until they get the Mod situation worked out. It'll probably be changed at around the time they get Steam Workshop integration working.
Luckily we've been able to work around that limitation with the type of modding we're currently capable of doing (RootTemplate and Stats changes) by just copy/pasting the different mod changes into a single blank mod.