On my Ember 2 pot noise seems more or less dependent on the amplification of the tube. Anything above around 50 mu causes some degree of noise. For 6DJ8, 12AU7, 6N6P and other low to medium gain tubes I hear no noise. For 12AT7's it's varies with the tube and with 12AX7 tubes there is always noise.
I agree, bypassing the IC's seems to give a marginally clearer more dynamic sound, but I need to concentrate to hear the difference, on casual listening I wouldn't notice a difference.
Anyway a bit of noise when setting the volume doesn't bother me in the least so I leave the IC's bypassed.