This is my exact experience as well. I'm using BSA 8.7, any info is appreciated.
Not sure where you're at with this. For now I seem to be having success with simply doing a *.* in the EXCLUDES of the affected parts in my component template I'm using for the audit job.
I don't know if this is something I can do for files with no extension in that I don't know if BSA can tell the difference between a windows file and a windows folder / directory, but this has got me through my immediate task.
I would prefer a filter to be applicable to the REMEDIATON job. that'd let me use 1 template for simple drift reporting AND for remediation, but I don't see anything that gives me that flexibility... hoping I'm wrong though.
the same template can be used for compliance and change tracking - just enable each operation on the part.