Can you set a new market without having to go there with a ship? - Yes. No problem there.
I guess that does make the game more realistic, though. Like, teh British empire did have small squadrons and naval bases all over teh World, after all.
Or do you normally do that, but only later game? - Later on, yes. And I agree that these new rules give better role-play.
I do think that you can make many colonies in a single system at least. Like, if there already is a squadron then having lots of colonies shouldn't really matter. Though, in cases where you have an A and a B star far away, and the two can't be connected by LPs, then you might need two squadrons. But like, between GTO, etc. then I think having lots of colonies in a single system won't necesssarily be bad. In fact, might be better to have many in a single system than having many across many systems. - Yes... but I like to access minerals in many systems. Popping out STO like candies out of a Pez dispenser sounds like the answer to protecting mining operations.