Hi Andrew, David
I have some reservations. The artifact from the dust line is worrying (There is a technical name for these isn’t there?). They wont be a problem in the sky background subtraction as they will average out but if they occur where the spectrum is binned they could distort the spectrum or at least give the wrong total flux. In fact a conventional flat would work correctly in this region, correcting the flux for the loss of light but the gain corrected flat would give the wrong flux even if the dispersion was exactly horizontal
Cheers
Robin