Diezel Einstein Master 1/2 - Do they sound different?

Basically I did the channel 1 mod, and use master 2 to match mega mode to the other two as I notice that mega mode is a little more compressed/quieter.

I presume it's just slight intolerances in the pots, rather than a voicing difference? I must stress, whilst I perceive slight difference, it's extremely minimal and minimised further at volume.

I believe you are correct in thinking its volume pot tolerance difference. Our ears change frequency perception with volume change so that could be the voicing difference you hear.