IIRC you can specify the coordinates where you start, so you could theoretically always start in our port even if your home base is not that one. There are mods that make the sub start at the dock OR at the subpens, so you can really put it anywhere you want -including in another port. The only problem is that unless you limit it to some days -when you start your career- you would be telported there again and again at patrol start even if you docked there the last time!
However this works great for "transfers" to the Mediterranean as you would start your career docked at Brest f.e. and have La Spezia or Salamis as your home base and a grid in the mediterranean to patrol. Once you end your patrol docking there, some days have passed and the game would move to a starting position in the proper place at La Spezia/Salamis docks.