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For LV, if you have time to do that, either implementation will work just fine. I have not much complain about either d700 or d800. While, d700, I can't do timer and MLU together.
For Matt screen, there is after market one available, and exposure compensation is easy.
As for focus confirmation, if you don't use how you deal with slow down shooting, Matt screen won't help you unless you shoot WO all the time. Actually, that is my biggest complain about adapt R to Nikon. I lose DOF focus advantage.
I am sure live view works well in a lot of situations with Nikon, but the decision to sample only some of the frames is an odd one and I wonder if it works well in low light. Perhaps someone who has used the Nikon live view in low light can chime in. I know some on the forum have complained a bit about Nikon live view.
The matte screen does help you even when you aren't shooting wide open. In my experience I just set the aperture that I want and I focus and compose at the same time and press the shutter. It is a very natural process and I don't have to worry about focus confirmation boxes and where they line up. To me that would be a huge pain. This works well if I shoot at f/1.2 or if I shoot at f/11. In natural light, if the aperture is set for a good exposure (i.e., proper exposure with enough shutter speed to prevent blur handheld), then in my experience there is plenty of light in the viewfinder. The only time the viewfinder is dark in my experience is if flash is needed to get enough light. With my fast lenses this just doesn't happen as even one shaded 40 watt light bulb with an f/1.4 or f/1.2 lens is enough to use the viewfinder. I suppose if under those very severe conditions you also wanted to stop down and your lens wasn't auto-aperture, then you might have a problem, but I have never experienced it. So, I simply just don't use focus confirmation ever and that I think is a big advantage.
I also think you don't appreciate the metering problems with after market focus screens. I find with my 5D MKII, that I simply shoot in A (aperture priority) mode, and the camera selects a good shutter speed based on the metering. This works well at f/1.2 and at f/11 and every aperture in between. The metering works great. With an after market focus screen, you have to dial in exposure compensation, but the amount of ec will change with aperture and lighting condition--it won't be a fixed set amount. You basically have to guess a bit and check the histogram. To me this isn't easy and is an annoying distraction. Having the camera correct the metering for the focus screen is easy and with the 5D MKII works very well.