> I think I’ll go with replacing instead of just reporting.

How about a --report-only (insert better name here) command line option to patchcheck, then?

My editor doesn't delete trailing whitespace *automatically*, but it's trivial to remove trailing whitespace from a file if you know it's there (M-x delete-trailing-whitespace, I believe);  some people (like me) might prefer to make all changes within the editor rather than having an external tool do it for them.  This is especially true if you've got the editor open for the relevant file at the time, since you can end up with two different conflicting versions of the file---one in the editor and one on disk;  saving in the editor can undo the changes that patchcheck made on disk.