Like, imagine if we let a bunch of aliens set up shop on the moon and they decided to rename it ‘Backwater Rockball 31’.
I never really thought about it but you’re right. It isn’t a federation station… it’s a Bajoran station the the federation are helping run.
Why doesn’t it have a Bajoran name?
I presume the Bajorans had their hands full with cleaning up after the occupation so they didn't care about the name. After all, it was just a rather irrelevant ore-processing facility.
When they asked the Federation to run the station, the Feds got to decide the name. 🤷♂️
San Francisco is where kirk found the past whales that saved the future earth, so the federation headquartered there in tribute.
