is it still easy to navigate without the rotary knob?

IMHO, yes. I only have a MkI myself but when I rode with Lars Karlslund (Wire) down to
Amersfoort I only recall using the knob for volume adjustments - could of course be that I'm
used to do any other stuff via buttons or remote...

and when you say the sound quality is a bit worse since the radio is built in, do u mean
the sound quality of the unit or of the radio only,

The radio only. AFAIK the DSP and output stages are identical in the different versions.
Even (especially?) the empeg guys say that they are not very happy with the radio in the MkI.
Hard to keep it unaffected by the digital noise the processor/busses/whatever generates while
inside the steel shell - or something like that

since there's no need for the radio with the empeg imo

Yeah, I bought a radio/casette deck as a stop gap thing for until I got the empeg; had both units
installed, but at the time I removed the radio/cassette deck I hadn't used it for apprx. 3 months
The radio in the empeg has probably been used twice besides setting up the stations...

/Michael