Well, that isn't a sensible answer, and of no use whatsoever to the OP. It clearly IS meant for zooms in this case, as it is specifically designed to use different adjustment at different focal lengths of the lens. If that is not meant to be used by zooms, what else is it for?
The 5D3 MFA can be set at the wide end and the long end of a zoom lens individually, the manual then states that it interpolates a third adjustment for the mid-range focal length. Thus giving three different MFA settings as you zoom, reducing the problem of improving one end at the expense of the other when adjusting with a single setting for the whole lens.
To the OP, I'm sorry but I cannot answer your question from any experience. I have the 5D3 but all my zooms are accurate enough that I have felt no need to MFA them. I would assume that the third setting has a set of algorithms which compare the long and short settings you input and come up with a suitable setting for the midpoint. I wouldn't worry where that midpoint is, as the MFA will theoretically be a sliding scale between the amount at each end and the 5D3 is just going to pick the best point for each lens.
However the 5D3 calculates it, it will be a significant improvement on using a system that only allows for a single MFA setting for the whole focal range. If, like myself, you would only MFA a lens that is noticeably out at one end or the other then you can now correct for that without throwing out the other end. If your lenses are not showing front or back focus issues at either end, then I would just leave well alone, which is what I have done so far.