Thank you for the link, V-B. Following on from that and other threads here and at TGP I get the impression - subjectively supported by my ears - that a modest cut in input gain does result in better humbucker tones, even with low output HBs.
The canary in the coal mine for problematic input gain seems to be the JC 120. It's surprising how many pickups sound bad with the pad off. Assuming that there's nothing unusual about the JC 120 model in Helix, this suggests that with the pad off, many pickups are hitting the front of the amp - any amp - hard enough to make a bit of mess that shouldn't be there. Of course this would affect all tones, all the way up to cranked, and a number of commenters think that it does (including me). So although it's an old chestnut (sorry), maybe worth a revisit.
If curious, I'd suggest to anyone wanting to check - try a few guitars through the default Jazz Rivet block with the pad off and on, dig in a bit with the playing, and see what you think.