1. Anything other than a capital ship is a support unit, so you could have a blend of SF, AUX, GAV, and INF as the PDF. This can help you balance your PDF, because in all likelihood we're probably going to see 1 Light CAP per system as a sentry... so it will need some help in space, especially at Outposts.
2. So if you play it smart, you can put a few AUX transport ships on PDF or use your capital ship to do evacuation assistance... or conversely, reinforcement (e.g. you can fully load a GR75, then keep it in orbit on PDF and when the bad guys come you can drop additional troops beyond the PDF limit -OR- you can keep an empty GR75 in orbit to land and gather troops). It takes a solid 3 turns to get from the X-grid to G-grids, so there is plenty of time to evacuate if you're worried you can't win a defensive battle. I suppose we could introduce a "depot" facility, but I think if you can creatively utilize capital ships and AUX, you can effectively handle a Battle of Hoth situation with the existing units.
2a/3. I think that's too micro-managing. Resupply is an assumed component of this game.