I've suspected that there were multiple configurations being tested as well. The "1DX top plate, 24MP and 12FPS" rumours were quite consistent for a very long time, and CR seemed to be getting those stats from sources they considered quite reliable. Moreover, for a long time the rumours stated that the camera would NOT be called 7D Mark II, which would fit if the product diverged so significantly in form from the original 7D. I suspect that two (or more) vastly different groups of prototypes were in the field, testing different types of technology and format.
As to the reason the existing form was chosen for production, there could be a host of reasons. It might be technical. It's possible the noise performance of the modified 20.2 MP sensor was better than the tested 24 MP. It's possible that a 12 FPS body didn't give the desired 200,000 shutter life, or it may have failed on other technical grounds. It's also possible that the 1 series design ethic didn't fit the expectations of the target market--enough people on here complained about the concept that similar complaints from focus groups may have resulted in Canon deciding to go with a more "5D" look and feel prototype.
It's also possible that the decision to go with the model chosen had something to do with target pricing. Many of the rumours associated with a "1DX" design ethic, 12 fps and a 24MP design also speculated on a $2000-$2500 retail price. That had a lot of people balking here in the forums, and also possibly in Canon's focus groups and market analysis. As a result, the winning design in the competition was one that could meet the requirements of the target market, yet still achieve a desirable sub two thousand dollar MRSP.
Pure speculation of course, but I think it makes a certain degree of sense. Not a conspiracy at all--just a pragmatic decision on what can be delivered for a given price point to the intended target market, without making that market too narrow to ensure success.
I don't concur though that the 7D II we are getting is in any way "obsolete" at all! I think it's going to be a phenomenal and well thought out wildlife/action/sports camera for the shooter who cannot afford a 1DX!
I also think the notion that they didn't go with a 24MP sensor to protect the 5D III is demonstrably fallacious. At the time the 7D introduced the 18MP crop frame sensor, the top of the line 1D III only had a 10MP sensor. And the 1DIV that followed in 2010 only had a 16MP sensor!