Final Cut allows for an extra level of separation called "Theme". It's a folder that fits this scheme:
Motion Templates/[Template Type]/[Custom Category]/[Theme]/<template folder>
Simply adding the theme level may or may not work for you. If a template is created with a Theme in Motion, the XML added to the template file specifies a theme, like this:
I have seen it reported that you can simply add theme folders and FCPX will honor it, so give it a try.
One caveat: If you've already installed and used templates from specific categories, moving them into theme folders will cause Missing Template alerts for projects/clips in which they were already used. If you used custom parameter settings, in most cases, these will also have to be reset. In this case, I would recommend copying the templates in the Finder and paste the copies into theme folders. (Verify the theme versions work). Temporarily remove the category level version and let Final Cut throw the Alerts -- they're easy to spot. ADD themed versions along side the Missing. In the finder, put back the temporarily removed versions. Go back into Final Cut and make the necessary parameter changes using the originals as guides. When everything is working without the originals, they can be deleted from the category levels, and restart FCPX to clear them all out.