That's what I was thinking. We have the Architectural Model linked in, so that could work, altho it is something that would then have to be changed any time we updated their model, so not a very good solution, unless their model is finalized.
Yes - I'd be a PITA, and it may come with unforeseen side effects. The easiest way to go about this would be to open the Arch Model, create a new Ceiling Schedule, add any one field, and disable "Itemize every instance". Now in the Schedule, you can click on the one cell that will be displayed and then on "Highlight in Model" on the Ribbon. You will then have all (except those on Design Options) of the Ceiling Elements selected at once, and you can then globally turn off "Room Bounding".
The only other possibility I can fathom would be to redesign your VAV box. Before Room Calculation Points, I had created a junction box Family that was intended to be placed above ceilings, which created the same problems that you're having now. What I did was build a "Custom Elevation" into the Family which would raise the model's geometry to the specified height, but keep the Family's origin within the Room, thus maintaining the association.
I emailed someone at the architecture firm to see if they would be willing to turn off room bounding for the ceilings from their end so I wouldn't have to change it multiple times. First reply was that they needed it to stay on so room names and numbers would show on their plans. I replied that I set my spaces to have an upper limit of the floor above with no offset, and asked if that would work for them as well, waiting to hear back. Your second solution sounds like a possibility. Would that complicate the placement of the the boxes though, when setting the height and matching with duct work etc.? I have an idea of what you're proposing, but not quite sure how you did it. If it's something fairly easy I may give it a shot, but I don't want to complicate things too much, as the other people working here are brand new to Revit, and I don't to mess anything up at this stage in the project. If worst comes to worst I'll just set the ceilings to unbounded in the arch model each time.
Basically, you'd have to create a new Reference Plane in which to host the Geometry, and then modify all of the relevant Constraints accordingly. Then, you add a new Parameter (Length/Instance) for the 'Custom Elevation' and create a Dimensional Constraint to the new Reference Plane. For this Family, do not use the normal Elevation Parameter, but rather this custom parameter. It's up to you as to whether or not you think this investment in effort is worth the results.
BTW - I don't think I'd ask the Architect to change their Ceilings and Rooms to accommodate this. I would just open the Arch and turn off the Room Bounding each time a new updated arch model was received. It's not that terrible, really.
I don't really see any reason to set the ceilings to room bounding, at least not for the architect. As far as I know they don't need any volumes to be calculated, and square footage wouldn't be affected by the room height. As for us, we might want the ceilings to be room bound for energy analysis, but we're doign that in another program.
I cannot do all the ceilings at once, as the room bounding option is greyed out. I have to do it floor by floor each time, and i also have to change the rooms to have an upper limit of the floor above with no offset in order to keep from losing them as well.