For the most part it does follow those configs, the only thing I can think of that it wont would be on the rewrite header flag. Otherwise, for qmail-scanner settings, you have to modify the script.
SA cant delete anything, you'd need to set that in qmail-scanner. I'm working on a new version that will separate all these settings into an independent config file, so changes will be maintained on upgrades. I should get this out in a few days with the qmail-scanner 2.01 release.