I can see how it will definitely make a difference with the Fort Dawnguard mod, as it is a pretty cluttered cell, but I started with the Bannered Mare because I thought it would be simpler (silly me). I am testing on a save in which I've already been to The Bannered Mare, but I've used resetinterior to clear it. I know this isn't sure-fire, but what I've done so far has shown up in game.
Here's what happened:
I decided to make three rooms. The main one, with the loft and the small room in the back included, then a second one off where the cooking spit is and a third, the mod-added room, which is next door to the one where the cooking spit is. By "next door" I mean these two rooms share a long wall.
After I made the rooms and before I made the portals, the interiors of both of the smaller rooms were invisible from the main room. After I made the portals, I could see into the room with the spit, but not the mod-added room. Unfortunately, much of the shared walls between the rooms was also invisible.
I'm thinking these shared interior walls are being counted as inside the mod-added space and, therefore, not visible with or without the portal.
I then cleared everything and started over, thinking I didn't create the rooms correctly and/or forgot to link the portals. Same effect. I then tried just creating a room bound for the mod-added space. Of course, there was nothing to link the portal to, so the entire second room was still invisible; however, this confirmed my suspicion about the shared walls, since they became invisible again.
The only thing I can think of is that somehow everything in the default Bannered Mare space is already considered one room, but everything added is not marked as part of that room, for some reason. Is there a setting somewhere that I can use to just select everything in the cell and have it be considered one room? I'll go back to the room bounds and portals when I start on Fort Dawnguard (when I've got the courage, that is).