I think there's a good chance the events of the Descent series could be between FS1 and FS2. The rise of corporations after the collapse of the Earth-based GTA fits well, and the CED probably arose from that threat. Technology seems to be at a similar level with Freespace 2, but on a different course. Note the CED Expediator in D3; missle tubes! A good chance of how Solar military technology evolved instead of beams.
As for the warp drive in D2, how did PTMC get to those systems anyway? It's possible those systems weren't linked by jump nodes to the rest of the galaxy so it would be impossible to get military forces or colonisation there. PTMC must have used its warp tech to set up bases in Zeta Aquilae, Brimspark, and the Limefrost Spiral without the GTA's knowledge or intervention.
I'm really disappointed that there weren't any crossover ships or weapons. Why can't somebody make the Pyro, Phoenix, and Magnum in FS2?

The only hint we get is that the Synaptic bomb in FS1 was nicknamed the "Earthshaker" according to the tech description. There was actually a great opportunity for crossover in Red Faction, too; for Ultor, read: PTMC. Makes a lot of sense, doesn't it? Particularly when there is a bloody mining revolt mentioned in the first Descent 1 briefing, which Material Defender apparently had a large part in. Since RF was originally going to be D4, a
prequel, methinks Parker was our very own Descent pilot, but all references to Descent probably had to be changed because Outrage's distributor owned the rights.