There is currently functionality being added to allow for custom portals to go to different dimensions, but I think it would also be very valuable to allow for different portal functionality if you are in a different world.
Say there is two overworlds, each with a nether dimension already created for them. I go to Overworld Alpha, and when I go through a netherportal it teleports me to Nether Alpha. I can replicate this in Overworld Gamma and be teleported respectively to Nether Gamma. It is possible this may be as easy as adding a "from" parameter to the portal command to override where the "from world's" portal's go to (depending on how you guys are implementing the portal command).

The portal command now has the option to specify the source dimension