Keith can answer in vastly more detail, but:
1. Yes, the Warden fleet is basically just a renamed special forces group. See the older release notes for how all that works, but basically there are resources given from the sentinels to the wardens. The wardens have an independent military mind, but their economy is subordinate to whatever the sentinels hand them, to my recollection.
2. This isn't really an issue either way. The sentinels do retreat, and you can see that in the video I made. But they have their own rules about that. Extra stuff that would have been "threatfleet" in the first game is I believe donated from the sentinels to the hunters. So the ships change color, which is handy, but it's the same ships now under new command. Something to that effect, anyway. The older release notes break it down to every last detail.
Hope that helps!