The only way to make missions currently is by using UFOs.
So:
- MiB fly around with their own "UFOs", which are just regular UFOs;
- MiB do terror missions which are actually modified UFOs;
- MiB build bases that are actually modified UFOs too.
Being all UFOs, they are generated as UFOs, not any differently than an alien UFO.
That's why the MiB mod, despite being the bigger, is the one I'm less happy about: it's a compromise.