I'm not flight crew (just ATC) so can't comment on any individual company policies, not will I step into security stuff. However...
You might be surprised at the number of flights which have crew in the jumpseat. I don't want to sound like a mad stalker(!) but we do sometimes check the aircraft out with binoculars as they taxi past the VCR, and there are very often at least 3 crew on the FD.
I assume it's mostly for line check or training purposes, which would potentially cover any route flown by an airline. I have no idea if uniformed crew ever reposition between bases on the FD, but that's another possible reason, and I'm sure there are many more that I'm not privy to...