[Polkageist]

"Make sense" is an interesting problem, since there are lot of things IRL that do exist that don't necessarily make a lot of sense. Maybe it used to and doesn't anymore ( So as long as there's a reason and that reason made sense at some point in time, then you can draw a line from each decision point along that point-of-interest's lifetime to the present day.

For world building (or campaign building), I like to start small and work outwards. You've definitely hit a key element, that the ship and travel are secondary and a method of getting from point-A to point-B without worrying about investing deeply (or at all) in ship combat. Totally valid, great way to keep the focus of the action in one realm. Also useful to use an existing property as a thematic grounding.

So, step by step process... I would probably start with the starting point. Where will the action start? A space station, ok.
From there, what else is nearby? Space station needs a purpose, so how about it being at a transit junction. Anchors a point in space, gives traveling ships a place to refuel and restock, maintains safety and security in the immediate area.
Next, I'd think a little bit about how people get around. Sounds like you've already got that fairly well defined: instant travel from point to point. I would guess also that there's real-space scooting around w/ some sort of drive for things like landing on planets or docking with stations. So that tells me that the action takes place around these junctions, because that's where people will gather to trade, produce, and meet, and that stuff doesn't really happen in-between ships in space really kind of like the same way that airplanes on Earth don't have encounters with other airplanes. You're on planet NYC and need to get to planet Chicago so you get on your space-airplane and in a few hours(days?) you're there.
At this point I may think about who's running the show. If travel times are relatively short, then perceived distance is small so a centralized government works. If travel times are long, then each location would be pretty independent and self-sustaining (i.e. fewer wildcat single-resource extraction colonies). This also depends on what kind of campaign antagonists I want, and how much involvement I want them to have. Since bounty-hunters (and not the bail-bondsman Dogg kind?) are a thing in your setting I'd probably lean towards a more factional and splintered up political scene that doesn't have a lot of resources to put towards internal policing. Or maybe the other way around, strong gov w/ robust legal system but with a lot of places for people to hide (spaaaaace) so you're Space-Dogg the bounty hunter and killing people is actually a Bad Thing.

But I digress. So far I haven't talked hardly about economics or 'how things make sense' and all about the major players and who wants what and how they get it. That's key. Unless the PC's will interact with municipal taxes, or the gross tonnage movable through a given port, or who produces what... don't worry about it. There are tons of historical examples of places that aren't economically viable but still people live there because they want to for whatever reason, or are economically viable but are just terrible places to be, or appear economically viable but only if you're really really lucky (klondike gold rush!) so there's lots of people there even if they shouldn't be. Also, as far as who produces what and how that keeps the system going... don't worry about it. Those places exist, but the PC's aren't interacting with them (yet) so you don't have to define them (yet).

Think about it like standing on a street corner. You're going to go into the coffee shop (first adventure), and you can see down the street that there's a hardware store and a restaurant (a couple places sketched out to go next), and you know that the next town over has a big brewery there (very loose detail about the larger world).

So there you go. Lay some things out in broad strokes so you have something to build on. Don't sweat the details until you need to, and let the largeness of the world absorb the oddities and quirks that might not 'make sense'. Improvise and retcon, if you make a mistake just fix it and move forward. Focus on the major players (of the plot, not the world) and who wants what. Plan ahead about three or four steps, but no farther because the PC's are going to upset the applecart anyway.