What is going on smacks, at least to me, of a "tops down" decision where executives have decided that the R1 will diverge from the 1DX line but they want a few more years to further develop the technology. Thus, we sit at an awkward intermediate stage of transitioning from DSLR to R-series when all the R-series bodies have yet to be released.
Canon is going out of their way to say that durability is a a differentiator, but "durable" is one of those relative terms. Canon's lesser bodies are plenty durable. I tend to shoot 5 series bodies and have never had an issue. But, they've said it enough I suspect there is some technical element to it. If I was to guess, the magnesium in the R3 may be thinner as a way to save weight, so technically, the R3 wouldn't survive a drop from the same height or something like that. Or could be that some of the seals are foam and not rubber. This is the type of stuff we'll only really know if someone like lensrentals does a teardown and compares the two bodies.
But, I would not be worried about durability if I was picking between the R3 and 1DXIII. Both would be elite, but perhaps one ever so slightly elite over the other.
If waiting for an R1, I am thinking it is a couple years out. So, it gets down to how long you want to wait.