I did a quick check and it works for me after adding these two lines:
CustomLocation1=FIREFOX|C:\Users\abc\AppData\Roaming\Waterfox\Profiles\xyz.default
CustomLocation2=FIREFOX|C:\Users\abc\AppData\Local\Waterfox\Profiles\xyz.default
It also cleans up the Internet History, even if it shows “0 bytes removed”. Simply check the modification date of the “places.sqlite” and “favicons.sqlite” files before and after the cleanup. CCleaner only cleans the database within the files, but does not delete the files themselves.