I would tend to the Nikon. Reasoning:
- Can be used on the A7r, Nikon or Canon body. Also if ever use for video the ability to control aperture on lens and possibly get 'declicked' by someone like Duclos will make life easy.
- It is plausible that until/if Canon comes out with a higher res FF body sans filter that the majority of DSLR demand for lens will be A7r / Nikon 800/e (or subsequent body) and video users (Nikon, 5DIII, Red, etc) - with the latter wanting on-lens aperture control.
Both preceding, especially the latter, would, amongst other things, aid any possible resale should you decide to do so years on.
Also, should (heaven forbid) Zeiss ever abandon the Otus line, value of a Nikon version will, plausibly again, be higher (assuming reasonable Canon mount build volume).
On the stop-down approach, I thought with an EVF body like the A7/r that as you stopped down the EVF brightness increased to aid focusing?