Apple knows most people are buying these machines to use full GPUs. As soon as you install a full GPU, you're bypassing the integrated chip. Then you're back to square one.
No you are not going back to square one. Most folks who want high powered GPUs want to hook them to "high powered" displays. Those displays have "mainstream" connectors on them that PCI-e GPU cards have. You hook the GPU card to the display and you are done.
Thunderbolt was, and is, 100%
pointless to getting that job done.
There is nothing that obviates having two GPUs any more than having two CPU packages is "bad".
In fact, some high end set-ups are going this way. Nvidia's Maximus solution involves two GPUs based cards.
http://www.nvidia.com/object/maximus.html
One card oriented to GPGPU and another oriented to the visual side of the problem. An embedded iMac class GPU isn't going to equal a Tesla card but the structure of the solution is the same. In workstation class problems this will likely be an increasingly common configuration format. It wouldn't hurt for the Mac Pro to have it as a standard.
It only takes getting past the x86 cores are the "only thing that matters" viewpoint.
Assuming that the iMac gets one of the higher end Southern Island GPUs
http://en.wikipedia.org/wiki/Comparison_of_AMD_graphics_processing_units#Radeon_HD_7xxxM_Series
A Radeon HD 7870M has a 1024 GFLOPs rating (that's single but even at a quarter for double isn't too bad). That is large enough to be useful even if there is not display hooked to the Thunderbolt port.
With the video output hooked to a normal PCI-e GPU card and a 1024 GFLOP real time compute engine available the Mac Pro could do some intersting things.
Similarly a Mac Pro with no high end GPU PCI-e card and two 16x cards could also do very interesting work ( e.g., 1 very high speed LAN and 1 x8 (or x16) direct attached storage (DAS) card; 1 Tesla card and 1 x8 DAS card ; etc. ) The Mac Pro isn't necessarily about just one GPU card.
If doing digital audio , crunching non video data , and a long list of other things then top end 3D performance doesn't really make that much of a difference.
It puts Apple in the awkward position of most likely selling an add on card that outright breaks compatibility with their own peripherals if you actually use it.
The notion of the Mac Pro as the primary vechicle of selling Thunderbolt Display docking stations is extremely dubious.
Even if want to go down that rat hole this is a cheaper way. Just have a BTO option with no GPU card. No you have a cheaper Mac Pro to sell so the user can more easily pay for their $999 docking statition with the entirely useless mag port connector.
Or Apple could make a somewhat more sensible move and .....
1. remove the power connector from the "regular" Cinema display.
(perhaps drop the web cam and maybe even the USB ports ). In fact, just remove the "attached fixed length" cable all together.
2. drop the price ( since it doesn't have to be a laptop docking station anymore ) or bump the backlighting and Display Port processing solution up so that is a full 10-bit color system.
and go back into making monitors. Not docking stations with monitors built in. The Thunderbolt and "general purpose" display could share major components ( LCD panel , major case elements , etc. ), but the internal elelectronics and connecting cable just differ. Apple could have two perhiperals just as they do now. Just two with better focus. The Display gets out of the docking station business and the Thunderbolt offering stops perpetrating that is designed for the Mac Pro (when it clearly isn't ).
I suppose my personal "Doomsday Scenario" is that Apple puts in some high end integrated GPU like what the iMac has, ends using discrete cards in the Pro line, and tells everyone to suck it up.
There is zero reason to nuke the discrete cards entirely. If that is the philosophy then they should just clone the HP Z1 and merge the display in also.