I was coming to the same conclusion re gain on binning > 1x1. I was indeed binning 2x2 on some narrowband shots to increase signal while keeping exposure reasonable, so the risk of overflowing the well in that situation was low, and controllable with exposure duration anyway. What threw me was the QHY9M/ASCOM camera settings dialog in MaximDL during initial setup - it invites you to store separate offset & gain for each binning, as though they expect a different gain calibration for each binning.
Anyway, I think I'm sorted for now, nearly finished the dark subs, about to undertake some more sleuthing. Thanks again Sander.