No one cares if it is thousands of kms apart. It only takes 45 minutes.
I think you overestimate the speed of a transport in-atmosphere. Traveller freighters are rarely streamlined and they can't make that kind of speed. to make hop around the planet means poking around in-atmo, or going up to the stratos or mesophere where the atmo is thin enough to make speed.
and pay twice the docking fees. If they are smaller owner/operators as you're are talking about, this will increase their costs.
Why would you assume that? It's not like a D-class port costs much to build - stabilize some earth or even pave it, set up a transponder and you have a port. Have a water tank and you have fuel. When you start getting into other size ports costs go up. Imperial ports would generally be MORE expensive to operate due to their needing to provide a lot more things than a private port might need (or want to do). And if the Imperium is willing to subsidize its ports then a nation might as well for multiple various reasons.
They won't be taking cargo from the big boys because all of the cargo for the big boys is already on contract. The little guys like Travellers have no contracts and all of the brokers are at the starport.
In general, probably not. Where they will take cargo is from the spot market or else from the direct market. Smaller freight companies that are established can regularly compete with the big guys on many routes - especially in the direct delivery market. They actually have an advantage there because they don't have the hub-and-spoke expenses. Being established or staking a claim on the smaller routes gives you opportunities that big boys can't compete on due to low volume.
Though as we've seen, if you are big enough and willing to take on the losses you can bankrupt rivals through legal, if unethical, actions. American did it to Braniff by paying a $10 bounty for every Braniff ticket sold by travel agents that was printed on American ticket stock. American had 90 days to pay Braniff it's fares and it paid on the 90th day. They starved them of capital and Braniff never could recover.
The Imperium doesn't care if your world is Balkanized, the starport is theirs and they will starve any competition to the Imperial port. Including "random" customs inspections while transiting to 100D, problems with ship registries in Imperial ports due to "possible smuggling activity", etc. Pissing off the Imperium isn't worth it for those who have to live and work within Imperial Space.
The Imperium has vast wealth, but they also have vast expenses. It won't operate a port at massive losses since it still expects every port to be more or less self-sustaining or a profit center. The Imperium is also supposed to be doing all this in order to make trade as even a field of playing as possible. It's entirely probable that they could, or even do, break their own rules when convenient. But as a general rule of thumb they are supposed to be the 'good' guys.
And I think we've already established that the IMPERIAL port is Imperium territory - but that's it. A planet with other ports may have significant traffic bypass Imperial ports all day, every day. The assumption being made here is that Imperial ports are the de jeure port in every system - and that just doesn't pass the sniff test.
Legally, up to the 100D limit is planetary control not Imperial. So long as you aren't harassing traders who declare transit to the Imperial port there isn't much the planet can do to those starships. Conversely, if the ship makes it to the 100D limit its subject to planetary laws - if it declares it's docking at a planetary port. This is a legal conundrum built into the Imperial design. The rules are pretty clear about the delineation between planetary rule and Imperial rule. In this case the planets have the legal right to tell Imperial vessels to stand down unless Imperial law is being broken. While the Imperials have the iron fist, they are also limited in what they use it on without triggering internal problems. No single system can stand up to them, but they also depend on the systems to not be in open revolt.
and the port on planet B would be a spaceport, not a starport. (In the OTU anyhow. IYTU it works however you wish.)
GURPS clearly calls out that other ports (non-Imperial) may also be full starports. Its canon-Traveller, not my Traveller. I quoted the GURPS section in a previous post.
It is several separate parts, but they are all considered part of the same starport with the exception of the megacorporate shipyards which have their own spaceport.
So at what point would a separate facility be considered separate? I have no issue with the downport/highport combo as two separate facilities but one entity. But by the same token you could have two downports and two highports (as well as additional orbital facilities located on an orbiting planetoid or at the 100D limit. Using the Glisten example, you may have facilities that are an AU apart. I would not classify those as being the same starport.
Maybe it would help you if you considered interstellar trade more like intercity trade. Stuff going to the city (destination world) from another city (the production world) is delivered to a distribution center (the starport). From there it is delivered to all of the local customers (cities, spaceports, and system colonies.. Traveling from the starport to anywhere on the same planet is 45 minutes or less. Those are city delivery times. Back at the starport the ship that delivered these goods will be loaded with other goods bound for another system. Everything is gathered at the starport so ships don't have to waste time travelling to more than one port in a system to get their cargo. Things are done this way because it benefits the Imperium and the Megacorporations, as everything they need is in one place. Money and power control the Imperium. That is why I disagree with what you call common sense, as it seems to not take human corruption into account.
We can use intercity as an example. And we can use trucks or rail as an example. Let's say I have a container being unloaded at the Port of Los Angeles and I need to get it to NYC. I have a few options here. If I put it on a truck I can have it driven straight through. If I have it put on a train I can also have it driven straight through on the same train. Both options take me a few days at least. Now, if I had say LTL freight - that's most likely not gonna make it straight through. Both truck and rail are going to move that cargo X distance to a hub where it gets unloaded and reloaded and moved again.
45min ain't gonna get you from LA to NYC unless you can travel 4,000 MPH. To make that kind of speed you have to be streamlined, at a minimum, and you are going to heat up like crazy at low altitude not to mention you'll be making sonic booms. To make that 2,800 mile trip it would be more practicaly to go vertical, then horizontal, then descend. I don't think it's reasonable to expect all that in 45min - let alone make a 12,000km trip. The notion that you can make Mach 6 in a ship equipped with a 6G drive flys in the face of aerodynamics. One can just look at the ship illustrations and see that the flight dynamics for some of these craft would be nuts. High-speed flight requires more than just brute force - which has many drawbacks as well.
What you are proposing is pure hub and spoke - incoming ships from outsystem woudl drop cargo at the highport/downport and then it gets picked up by the planetary network for delivery onplanet or insystem. I thought I had stated that this will work for some of the cargo. However hub-and-spoke cannot economically compete with point-to-point across the board. That is impossible and illogical. I can pick up my 50dtons of cargo in my Free trader at Port A in system A and deliver it to spaceport ZZ in System B directly rather than drop it off at Port B in System B and then have someone else have to pick it up and fly it somewhere else on the planet, or say 2 days out to Planetoid ZZ to drop it off.
For some the system you are proposing works because you don't have to think about it and you don't have concern yourself with the actual process or logistics. Things magically work and everyone is happy. Others might want to actually to game this out because they are looking for more opportunities to adventure, encounter, or whatever. Having clear explanations on how it works, for both large and small, can be an important (and fun) detail for some, or needless blah-blah-blah for others. But if it ain't in the books you can't do any of it well unless you want to devolve to IMTU - which if you are paying for a great supplement like GURPS Starports, then I expect them to have it detailed out to some degree (which they did).