Brad, I believe you are correct in that the channels aren't mixed in any way. So, maybe consider the RDES as dual mono. To me, if a product is stereo, then each channel should act independently of the other. Since the RDES applies the same correction to both channels, it is far from being true stereo.
But, semantics aside... the real problem is if you try to use a single RDES to calibrate stereo subs, you may create more problems than you solve. Stereo subs, unless they are placed perfectly symmetrically in a "perfect" room will each load the room differently. What the SPL meter then sees is actually the potential summed response of both subs. The resulting corrections may not resolve the actual loading issues since the stereo subs can mask each other. You need to be able to adjust each channel independently.