To me, it would seem logical that this should then be the secondary purpose of building a commercial spaceport. The primary purpose is to increase load and unload speeds for queued civilian ships and the secondary purpose is to be the HQ for new shipping lines launched.
Number of spaceports built on a planet then becomes the number of civilian lines that can be supported. If you have a colony 12 jumps out with viable trade opportunities then build a spaceport and civilian industry will found a line and build ships.
(maybe this is how it works and I am naive)
This is not how it works.
The civilian industry is both my favorite-- and least favorite-- part of the game. I feel like we need any of 3 big improvements:
a) storable paths, similar to the sector assignment screen, that would shorten the amount of pathing searching a civilian ship would have to do. I feel like civilian spaceport level could increase the "range" in much the same way as sector command level does.
b) setting headquarters for civ industry in the way you describe, which would give ships a home base to return to if lacking jobs. This would prevent stagnation of the fleet, because different fleets could have different homes, so goods could still move around.
c) infrequently-- maybe every 20 construction cycles, for instance-- every stagnant research vessel searches beyond 4 jumps for an available job, and if none is found, path to home base (earth, but would work great if we could assign fleets to headquarters).
Any of these three solutions would, in my opinion, help.
I also want ancient ships to scrap themselves, and I'd love for civilian industry to band into fleets of like ships, perhaps each line could only have 70 independent task groups-- but those groups could hold an infinite number of ships. This would reduce pathing requirements in late games.