My first 5D3 had an issue that the AF points were calibrated differently - that is if I calibrated for the center cluster, a lens might need 0 MA but if I calibrated for the right hand cluster of cross points, a lens might need +8 MA. So everything I shot with side points were waaay off in focus (horribly off). Second copy of 5D3 is much better.
I would definitely MA all lenses. Just a few MA points makes a big difference on these higher resolution sensors.