You can have a 'main' base or several. Their location doesn't really matter because you have portals. Usually, my criteria for choosing a location boils down to something like, this would be a good spot for a dock, or this spot has a great view, or this spot has a large open area I can kill all event raiders ;)
Before you say anything about not being able to transport ores through a portal, just smelt them on site, craft them into the finished product and then transport what you make ;)

Alternatively, you could just world hop... Carry everything you want to transport to another world, hop back and then portal home, log back in to the other world and carry everything back over to your world ;)