From what I've seen in most IMAX scenes, the way they get around it is by not doing zoom thru shots or long distance shots, thinking about Space Station, Hubble, To the Arctic, Grand Canyon, a few that I've noticed this where no zoom shots are included. It's more like they set up a shot, usually wide angle and do panning or tilts, but not much with distance variance, unless they change the location of the rig. With beam splitter setup, the same problems arise with zooming but if they're genlocked right and a motor is applied to the horizontal I.A. adjustment, zooming is possible, it just has to be controlled correctly. And depending on how large the mirror is.
I don't know if the IMAX systems are capable of zooming or not. I'll have to pay more attention, but thinking back I don't remember seeing any. Lens replacements don't seem like a possibility with the close proximity of the lenses just like on the 3DA1, there's not much for lens adapters out there. Looking at the digital IMAX rig it appears those are the actual lenses and not the sensors.
Another big advantage with mirror setup is that different lenses can be used, here it seems like you're stuck with the integrated lenses just like consumer rigs. Not that I have a problem with that, since it adds portability and hopefully ease of use and cost, just a limitation, although in a big production environment like Transformers I would think that'd be a major limitation.
Really hope this opens the door for more production of all in one units (consumer versions) for us that don't have a large crew running a 3D rig. I haven't heard of any new units being released, hopefully they're not yesterdays news. Maybe the all in one mirror rig is far from thought right now from manufacturers but I think it would work and really open the range of 3D filming.