You can make a mask and apply it to the image before you use SXT. Then those regions will be protected. The most recent examples of this demonstrated are in the comet videos (where you need to protect the core of the comet when you do batch SXT on the calibrated data).
Just make a mask... and give it a go. Nothing complicated here.
Another trick (from SetiAstro) is to clone stamp away the nebula from the stars-only image; hit undo on the starless image to bring back the stars; now subtract the "clean" stars image from the starless image.
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