Sounds to me like you've never actually used a different focus screen on your 6D, and you're obsessing about something you've read online.
Just get the super-precision matte screen (Eg-S).
I've adapted manual focus lenses to both my 5DMkII and 50D--both of which have the same interchangeable focus screen feature your 6D does. Swapping the focus screen is relatively quick and painless, as there's a small latched door--unlike the dRebel models, where the screen isn't meant to be changed.
With my 50D, I used a split-circle focus screen (Katzeye) with my manual focus lenses, like my OM-mount 50mm f/1.2. But because the prism collar (NOT the entire screen) blacked out with f/5.6 lenses, whenever I went birding with my 50D and the 400mm f/5.6L USM, I'd swap the screen back to the default matte screen that came with the camera.
However, being lazy (and cheap), when I got the 5DMkII, I decided not to go with another Katzeye, but got the Canon Eg-S "super precision matte" focus screen instead. It works fine at accurately depicting the DoF for f/1.2 wide open, and, while it's slightly darker than the default screen, it still works just fine when I use my 400/5.6 or 24-105 f/4L IS USM. The custom function setting for the focus screen is merely to help adjust the metering. Once I swapped in the Eg-S, I never swapped it out.
To my surprise, the accuracy of manual focus with the super precision matte screen is equivalent to using the split circle screen. Something I would not have expected from my 20+ years shooting a film SLR with a split-circle screen.