Yes, of course. Now, custom BG levels will be a bit dangerous to run, as Multimedia Fusion 2 doesn't have the option to disable file writing actions that might be present in sub-applications. This means that the level designer can in theory use Multimedia Fusion 2 to build a virus into the level add-on modules, and there's nothing I can do to prevent it.
By this reason, I might not officially support the idea about running third party levels at all, but that it will still be available at your own risk through using a command line. The level designer shouldn't have a problem creating a shortcut file that runs the program with the right command lines though, I know I have seen shortcuts that manages to use relative paths.