I have an idea to make a separate database (or only table column in DB) for the creations from mods. There would be no compatibility issues and you could publish creations without any problems with official client. Any (accepted by admin) developer would be able to register own mod that would be presented at login as some "MOD_ID". Search results would have been displayed only for the specific mod.
EDIT: sorry for grammar, but my laziness wins in the presence of google translate