1) Refuelling Systems and Ordnance Transfer Systems are conventional tech so you start with them in a conventional game.
I'm not sure you should. The Spaceport isn't in conventional starts in 7.10, and given the BP (and presumed mineral) cost of a Refueling Station and an Ordnance Transfer Station these should be gated similarly.
2) Not sure what you mean here. Each collier or tanker has a set amount of transfer per sub-pulse and can't exceed that (even if it refuels multiple ships). Each ship also has a max transfer per sub-pulse limit (which is set to the max transfer rate of any ship trying to refuel or rearm it), so you gain no advantage in trying multiple refuels in a turn.
Didn't rules use to be 'every refueling system refuels at max rate'? Because it appears I either misread or that exploit was closed. If a collier or tanker cannot exceed their highest rated transfer system... well, it means that multiple refueling/ordnance transfer systems are no longer a thing, but at least you can't stack multiple tankers or colliers, or such ships carrying multiple transfer systems, to allow much greater transfer rates.
3) I want the spaceport to be a major facility. It combines two 1200 BP stations, plus the cargo handling. Plus I might give it some other ability before the game is completed.
That may be so, but for the cargo handling alone it's not really worth expending 3600 BP for a level 2 spaceport. I mean, 3600 for the cargo handling and unlimited resupply links is an expensive but worthwhile investment, but you can get that same result
and no worry about wasting resources by keeping the spaceport limited to cargo handling alone. I mean, at 1200 BP it's already a pretty major facility, but at 3600 it's the most expensive thing in the installation construction menu and beyond a level 1 spaceport all it does is add to the cargo handling modifier.
Useful, but for a system that will require 1.5 times the Build Point cost of an Academy, Lab, Shipyard, GMC, GFTF or Sector Command that's really quite expensive and the only reason that cost increase seems to be happening is the mission creep of spaceports. That's not counting the 8 times greater amount of shipping that's needed to get a spaceport where it's needed compared to a resource transfer station either.
Easiest way to handle the expense issue is by simply removing the mission creep. Let the spaceport remain a 1200 BP cargo handling facility, the resource transfer tasks can be handled by the dedicated facilities of the same costs. It's a little more fiddly at first blush, but you're going to be juggling fuel and ordnance transfer stations anyway, and this way you don't need to worry about doubling up on transfer capacity because you also have spaceports with the same ability. The only question you need to ask is if you have the appropriate type of the transfer facility on planet.
4) The Spaceport, Ordnance Transfer Station and Refuelling Station are all ground-based facilities and also conventional tech so there is no problem with a non-TN start having them.
The spaceport is not available in a conventional tech start in 7.10.
With regard to the PDC, I am seriously considering removing PDCs from the game. They create exceptions for a number of rules, confuse new players, add complexity to ground combat without necessarily adding a commensurate improvement in game play, and their maintenance-free status can be an exploit. I may replace them with some additional types of ground forces to improve defences planetary defences and keep all 'ships' in space. One of their major advantages is to allow maintenance-free bases on new colonies, but even that is no longer as great an advantage given the new maintenance system (you can build orbital bases that can provide their own maintenance facilities and just ship in supplies).
Eh, planets need some level of viable anti orbital attack system, and I'm not sure ground forces can provide that. A station might, but you'd need to research stealth to get a station that can provide a decent surprise to a committed enemy.
Then again, early sensors are... not that great. You might be able to do quite a bit with a station with good passive sensors and a good firing computer if you've got seeking missiles, but, well, early sensors are crap.
To be honest, PDCs seem to serve two major purposes to me when you get rid of the methods they let you cheat the maintenance system. The first is anti orbital combat ability through slinging missiles and energy weapons at enemy ships. The other major purpose is slowing down enemy occupation by forcing the enemy to siege PDC after PDC with ground forces, or by denying them the planet altogether because of the collateral damage done by orbital strikes to root out the defenders.