Interesting post by troywright on AUGI, in relation to setting up segregated links as room bounding in your Revit MEP file:  
We have this issue frequently, as with major projects we will receive different models for architectural fitout, shell and core and facades etc. 

The solution we have (in your example) is to; 
– Link the structural model into architectural as an overlay, set to room bounding 
– In your MEP model link in the structural model and the architectural model. 

That’s it. Essentially it is an extra step, but it means that the architectural model knows it is bound by the structural model, even though it is only an overlay! I think someone else mentioned this method earlier but with worksets. I can’t see a point in doing this as the nested structural model is an overlay, so it’s irrelevant. 

Another issue you may have is that your spaces act up when an architectural model has floor finishes set to room bounding that are higher than the level they are on. To fix this just change all of your levels to have a calculation height above that of the floor finish.

via 2014 MEP Spaces

Revit MEP users have had access to Embedded Schedules for a while now. However, the Revit 2013 OneBox version gives everyone the ability to easily utilise Embedded Schedules.  Have you used them yet?

Embedded Schedules are available for the following Categories: Rooms, spaces, duct systems, piping systems, or electrical circuits (do you know of any others??)

Architecturally, it makes the most sense to use a Room Schedule or a Space Schedule.  If you opt to use a Space Schedule, this means you will need to add Spaces to your model (Subscription users may want to take advantage of the Space Naming utility).  Once that is done, you can then Schedule Rooms IN the Space Schedule (first image below), and then create an Embedded Schedule for Doors, for example.  This will show you which Doors are in which Rooms.

Check out the images below.  In the third one, I use a calculated text value of “” to ‘indent’ the Embedded Door Schedule, to make things a little bit easier to understand.

A nice little benefit of adding Spaces is that you can also take advantage of Zones (HVAC Zones).  Architectural users may re-appropriate Zones as a way to sort and group Spaces when doing a multi-building, single file RVT model.

Room details added to Space Schedule

Embedded Door Schedule

A little trick to indent the Embedded Schedule

Read more at:
http://wikihelp.autodesk.com/Revit/enu/2013/Help/00001-Revit_He0/0004-Introduc4/0042-MEP_Esse42/0059-Embedded59/0060-Creating60

Pre-2013 OneBox RAC users can add Embedded Schedules in RME2012 and then re-open in RAC, as per:
http://wrw.is/2011/11/embedded-schedule-workaround-for-revit.html