That was more or less the impression I got. My point was that if you take the rotary encoder input into the CNC controller and let it send the pulses to the correct motor. This way the CNC controller always has up to date position information. Of course this implies CNC controller software that can handle rotary encoder input for this type of operation.From what I read, I think he wants to be able to easily switch from CNC to manual operation, but have the handwheels operate electronically. I know I wouldn't want to manually machine anything on a CNC mill simply using jogging. I can see where this would be useful as well - if you've only got one machine and want to do a series of simple operations on a part and don't want to generate g-code, flick the switch to manual and have at it. Then, when you're finished, flick back to CNC and run your next part. If I was going CNC I think I'd be interested in something like this as well.
For manual "CNC" milling the CNC controller is a great substitute for an axis drive of old. Instead of having to guess your feed rate you can set it directly and tell an axis to move X amount of inches. In effect you use the CNC controller like an old mill with powered feeds on all axis. Frankly it is only slightly different from engaging a axis feed lever on a large mill. It is one reason why I encourage people to learn a little bit of G-Code as you can often save a lot of time and gives you more flexibility at the machine for Non CNC projects.
I can see both sides here but I'm not real excited about the idea of having a bunch of loose knobs on the machine that could lead to unintended axis movement.