I don’t find tuning difficult or time consuming for the most part. I guess it depends on workflow, though.
Generally I tune by ear, and tune voices relative to each other. I wonder sometimes how people with perfect absolute pitch perceive my music 
If I have a less flexible voice that doesn’t transpose easily – like an exponential FM voice – I’ll adjust everything else to match it. Sometimes the easiest way to do that is to use the O’Tool+'s tuner to match a reference note through the MIDI-CV interface.
If I’m going to sequence within the modular system instead of via MIDI, I’ll usually tune the VCO so 0V is the lowest note I’m going to use, or maybe one octave below the lowest root I think I’m going to use. On those occasions when I transpose CVs I tend to do it with a summing mixer (a “non-precision adder”
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