This may seem like a silly question but... shouldn't that problem be moot when using focus peaking? Since we are looking at what the imaging sensor ACTUALLY "sees" is "in focus"?
It is moot when you are using Direct manual focus (DMF) as the camera performs it's auto focus then drops into manual focus and the user adjusts it to compensate for focus problems using the focus peaking. However focus peaking in AF mode does not compensate for a camera or lens that are out of adjustment. Focus peaking in MF mode does. The proof? Why would Sony supply the focus micro adjust feature on the A77 if it was not needed.
Cholly, I answered your question a few hours after you asked it.
Sony A7, A850, A77, A700 || Sony>> 70-300G, 28-75 f2.8 SAM, 16-80CZ, 50 f1.4, FE 28-70 OSS, FE 24-70CZ f4 OSS, LA-EA4 || Minolta>> 300 f4 G HS, 200 f2.8 G HS, 100 f2.8 (D) Macro, 50 f1.7, 28 f2.8, 28-135 f4-4.5, 70-210 f4, 500 f8 Reflex, TC x 1.4 HS, TC x 2 HS. || Sigma 21-35 f3.5-4.2. || Tamron SP 24-135.