Why would Canon (or anyone else) have any sort of need to differentiate camera bodies with sensor technology. The people who buy this sort of cameras are people who buy them to use them, not be amazed by the price that they can afford to pay, or by the technology that they have and the mortals can't afford.
Canon / Nikon / Sony make money through mass production. Take nikon's D4 and D800. Nikon says that D800 production will be 6 times that of D4. That is, they expect to sell 6 times more D800s than D4s. At half the price, that makes 3 times the revenue. They don't care about differentiation because more people buy the lower priced body.
Also, the price of having sensors with (truly) different technologies is simply too high to justify bothering with it. Production of high precision mechanics is far-far-far more expensive than mass production of microchips. A 1D body is, as Canon has put it, a high precision mechanism.
In fact, I say that 5D3 will have better sensor technology than 1DX... but that only shows that the question and its intended meaning are conflicting. Each camera will have the technology for the intended purpose.
If you are implying that one of the cameras will have worse looking images than the other... the question is - in what context? Noise level, noise characteristics, photos, movies, usage of more stable and more expensive materials?
Consider that the rumored maximum analog ISO for 5D3 is 25600, for 1 DX is 51200. However, Canon has implied that 1 DX has 2 extra stops better noise due to the noise reduction. Since 1 DX has two image processors, it's reasonable to think that the extra stop comes from the noise reduction power given by the extra processor.
So, based on no physical evidence, I say that the noise levels for the two cameras will be similar for the same ISO.