Thanks for your post.
This request has been added to the tracker:
https://winscp.net/tracker/761

Actually you can use the exclude mask on copy dialog to exclude the files you do not want to copy, despite being selected when comparing directories.

Hi

First a big, big thank you for WinSCP. As a developper, this wonderful tool is my link between Windows and Debian's for so many years now that I couldn.t leave without it :D

That said, I would find very useful if the "Directories comparison" tool would be smart enough to use the same files mask as the "Copy" tool, at least as an option.
Indeed: the comparison often result in a copy process, and some files are uselessly pre-selected.

Sorry if I've missed that option if it already exists...