Short update: Installed Catorise and while it does modify hildon.menu, it uses the system-wide instead of the one in your home folder.

So, IN THEORY one could at least safely switch between both applications (deactivate ApMeFo to use Catorise, activate it to use ApMeFo). Sadly, for some strange reason some of the applications will still be displayed in the main menu despite being put in custom folders. Not sure why this happens, as the user hildon.menu should completely overrule the system-wide one.

Well, at least neither one of the two is harming the other (once I removed Catorise, ApMeFo was back to it's normal behaviour).

Oh, and it seems Catorise DOES use the system described by lemmyslender, so once it is included you could at least get similar results to Catorise. Just by far less comfortably so...