You can set the offset for manual lenses as well - it adjusts the focus confirmation set point and is very helpful. The only difficulty I had was with the 300 APO, where its near focus setting wasn't the same as the far focus. But in general, it is used for all my manual lenses and the 80 AF. I use a digital back, and check the offset typically by tethering or chimping.
No AF problems with my Hy6 mod 1 - but its firmware was updated by the factory, so maybe that helped.
And yes, the 60 Curtagon is stellar, have used it since the 1990s. So too is the 90 (since sold), and the 150 4.5 is something special. They all have their charms.