What do you mean by manual focusing? as in auto focus during video?
3rd party focusing screens?? Im guessing the answer to this one will be, what was the situation with the 5D2 and 7D? It will probably be the same with this as they are basically a combination of this camera now body wise.
by manual focusing i was talking about the ease of focusing (and judging DOF) using a fast lens with the standard focusing screen. the standard focusing stops accurately showing DOF any wider than f4, so even if you focus accurately on your subject using MF or AF you still won't know how much
of your subject is actually in focus. i agree that the AF is really fast and accurate, but that doesn't help you when you're using a Zeiss prime, for example, or even the 50mm f1.2 if you're using it wide open.
thus why i was wondering about 3rd party screens. if you install a 3rd party matte screen focusing with manual and fast lenses will be a lot easier because DOF will be much easier to see. in addition to what Pyrenees said about metering, the problem with installing a 3rd party screen is potentially voiding your warranty.