Update: Well here's a thing. I've been using the Trace Combo for every rehearsal and gig since I got it, and I love it and everything about it - so do the band. Last rehearsal went particularly well and I silently congratulated myself on a great choice of amp, then patted myself on the back for really getting to grips with the legendary Trace Graphic EQ. Only... when I got home I realised the graphic circuit had been switched out for the entire rehearsal.
So Trace made their amps to sound best completely flat, played live in a band setting. Who knew? This would explain why the manual would have you make only very small changes to the graphic sliders, and not move too far away from 0db! Every day's a school day...