Now that I’ve moved to FSE themes, there are things in functions.php that are not needed. There is also the issue of include inc/custom.php not being at the bottom of functions.php (see previous feature request).
In short, it would be great if we could control which areas of funtions.php PG handles. Right now, I get error messages in PG if I try to remove sections. It would be nice if PG could just skip if I’ve intentionally removed or reorganized functions.php. At the very least, it would be nice if I could just format my own functions.php that overrides the default one.