I have similar problems while working with wider FOV images. Either a lot of stars remain at the comet integration or if I go too far with rejection, the comet does not get subtracted properly. Also the "stars" integration has a wilder background than a typical integration, which is hard to fix.
My feeling is that the normalization with LinearFit (during the CometAlignment comet subtraction phase) is inappropriate and a better solution must be found, probably using LocalNormalization, or a scaling based on a ROI utilizing the comet only and not the whole image. Why subtracting something from places where there is nothing to subtract?
Any advice will be welcome.