It's odd that you couldn't get the levels to load. If you have the latest version, they should be working. Though it's possible that there's something there that hasn't been patched out yet. It's also odd that you were able to play the original levels, since the mod is supposed to have its own set of levels. Unless you just copied them into the mod's folder.
To answer your questions:
- This is never explained. I always assumed that Mental just has some magic or technology, that lets it sense energies and detect advanced civilisations.
- Some factions might follow it, because they think they have something to gain. Usually that gain is a lie, or a pact made with the worst of that species' society. Other times its forced servitude.
- Sam isn't the last human. This time SS3 ends differently and humanity successfully repels Mental's attack.
- The Sirians aren't humans.
- The SS2 medallion is entirely useless.
- There isn't one specific Discord for the mod, but there is an active thread on the Serious Sam Classics server.