Steve,
They can have a significant effect since you are stretching an unbalanced background that can create a fair amount of havoc when what you are trying to get is a smooth, grey background in your final image. There are lots of tricks to help with that process, but recently I have been taking a different tack and waiting until after I have stretched the channels before combining them (several methods you can use but I like the result I get with the SHO-AIP script).
As far off as your numbers are in the linear stage, you may want to try both methods to see which produces the best results. Note you can also use Linear Fit after stretching. The trick, however is making sure that linear fit or any other method used to fix the background doesn't mess up the color balance of your nebulosity. That you manage with masks, protecting the area you DO NOT want to change and that's a good solution in both the linear and non-linear phases of your processing.
Best,
Jim