First off, all lenses focus when they are wide open, however that isn't the end of the story. AF modules have an effective aperture, Canon AF modules have been said to have an aperture of f2.8, just like the standard focusing screens have an aperture of f2.8 or so. Ever tried manually focusing an f1.2 through the viewfinder? It is very difficult because you are seeing a dimmer and deeper dof view than the lens actually is. Put your lens to f4 and push the dof preview button look through the viewfinder and take your finger off the dof preview button, that is the difference between what you see through an f 1.2 lens through your viewfinder and the AF module 'sees' through it's opening, and what the sensor sees through an f1.2 lens.
The fact that the AF module has an aperture slower than the lens doesn't mean it can't focus it accurately though, it just means it is more difficult for it to see than it needed to be if it had a wider aperture. Don't forget dof is considered to be a range of 'acceptably sharp focus', any mirror down DSLR AF system will always try to attain maximum contrast which should, in ideal situations, be the plane of focus you actually want.
AF module aperture and focus breathing have nothing to do with each other, neither does AF module aperture and lens aperture until you go the other way. Once you get to slow lenses wide open at f8 the view for the AF module becomes so dark it can't reliably attain accurate focus, it is looking for contrast but the lights are so dark there isn't enough, hence the slowdown in AF speed when we use TC's, and why some people find f8 easy to use (bright sunny day with a 100-400 and 1.4 TC with a high contrast bird in the sky), and some people find it totally useless (same lens but very late afternoon trying to focus on a bear in the woods, lower light levels and much lower contrast).
So:-
1/ All lenses focus on our DSLR's wide open (unless you are using old lenses and stopping them down manually).
2/ Anything that views light has an effective aperture (viewfinders, eyes, etc).
3/ AF modules have an effective aperture.
4/ The AF module aperture does not limit its ability to attain highest contrast, which is normally the plane of sharpest focus, ergo an f2.8 module can accurately focus an f1.2 lens.
5/ Focus shift has nothing to do with AF.
6/ There isn't an offset value to which lenses are focused after AF has been achieved to allow for focus shift.
7/ Focus shift is an intrinsic design element of a lens.
8/ Focus shift can only happen when a lens is stopped down.
9/ Focus shift can only be noticeable when the dof doesn't cover the shift distance.
10/ DOF gets greater the further from the camera.
From all that we can know that only fast lenses stopped down a modest amount at closer focus distances with an intrinsic design will display noticeable focus shift. Many will use their 50 f1.2's and never lose a shot to focus shift, many, generally who don't own or use one, will forever worry about the shots they might lose never considering the shots they can't take! Very few people who use the 50 f1.2 do so in such a manner that the focus shift is so problematic as to be unworkable.