The ".mod" tag is counter-intuitive. I had to go looking for an answer to this, too; they should probably put up a sticky thread or something.
A ".mod" file is really just a swf file. There are swf mods that only work in the Loader, so some people change the extension of their Loader-only mods to something that only the Loader knows how to read. That prevents people from mistakenly running them in the normal version of SDT.
(It's an annoying practice, but it's also annoying to download a new swf, try to run it in the normal version, not have anything happen, and have no idea why.)