Unfortunately there will be issues if a modifier tries to create two cameras.
For the moment, you can use the V-Ray stereo rig controller, which allows you to have different stereo settings for your cameras, and it creates two separate cameras for each center one.
Yes, some more control would be useful, but you can already do this pretty easily (f.e. by assigning look-at targets of the left and right cameras to be the same as for the center camera).