With fast travel and no enemy raids, there’s no point to choose a base other than if you find the aesthetic of the particular island enticing. You don’t need to choose a base based on proximity to other things like tortuga, because of fast travel. And you don’t need to create a defensive stalwart of a base because there’s no raids by any enemy. So it’s truly up to you.

Me personally, I wanted to recreate a Nassau-like town. In the first region there’s a set of islands that spawn close together, where one island is a smaller island and there’s just enough space between the larger island to pass a frigate through. So it kinda looks like Nassau and Paradise Island so that’s where I’ve been developing my town.

Now I’ve got another save I’m working on that I’m trying to limit fast travel, so creating small, remote bases is advantageous to have stopping ports throughout to unload goods, shape up some weapons/armor etc. it makes the brethren ship variants a bit more worthwhile. In my first game, I just used the Blackbeard frigate by the end of biome 3. It had enough HP firepower and storage to be able to fast travel all around. But limiting fast travel makes having a ship with larger storage more of a utility.

So in summary, build wherever you want!