1. I cannot find a definition of exactly what a commerce centre does, Jeeves' economy guide doesn't mention them.
2. If a commerce centre simply buffs trade by x% then the real question is what defines trade on a planet and how do you determine how much it is?
3. From what you say fuel is distributed to all bases, whether starport, star base or defence platform?
4. The basic rule of thumb is if you don't want to build ships at a planet, don't build a starport?
The main issues I'm trying to figure out around this question at the moment are these:
A. I always seem to have enough resources to build ships at HW (where I have the Bakarus) but the LSP there is always running out of fuel to fill up new ships, and most other starports run out of it as well when I'm running military campaigns. I want to fix that somehow.
B. I am struggling to figure out the trigger point to build a star base/defense platform on planets, or how to design them, that I don't want to build a starport on. I get the happiness bonuses from rec/med when I want to tax the colony, but i can't understand the benefits you get from a commerce centre or how to gauge how many docks are required for a planet etc.
3: All facilities at colonies share the colony's storage. Fuel is distributed to colonies, but probably more of it is sent to one with spaceports, and more is requested the larger the spaceport (not size, but if small, medium large).
4: Calling spaceports for starports does not make this less confusing ;-) I would build spaceports when I feel the need for another one. A need grounded in more capacity for ship building, a new location for ship building, or a location for repairs. I would resist building based on repair need from early pirate annoyances somewhat near the capital, though.
A. Make sure to build a gas mine on any fuel location remotely near to the capital. How much fuel you drain probably depends on your economy and way of playing. Slower games give more time to store fuel. Losing more ships in combat and having lots of automated ships running around drains more fuel. Deploy resupply ships in systems where you have fuel issues. And don't add new builds to active fleets if you suspect they may be built with no fuel. Have them refuel at the local resupply ship first. Is one resupply ship not enough? Deploy another one, you should be able to fit several resupply ships and a gas mine on the same gas giant.
B. I don't mess with ship designs, but you don't really need docking bays if you have no spaceport. Colonies have a lot of docking capacity, but should be a bit slower in moving cargo. If you capture a capital, give it a spaceport, for other colonies, a number like 6 should probably more than enough docking bays.
Why a spaceport at a former capital? There is probably a lot of resources stored that other, including foreign, colonies want a piece of.