Is there any real difference between how the AI commander uses these 2 groups?

I assume the spec ops groups are supposed to be your recon teams with suppressed weapons, but will the commander actually do anything different with those groups?

Yep I would hope that can happen pretty soon. Because at the moment you have to run them as specific groups or factions if you want to use them differently; or at least it is the way I have done it and seen it done.