My use case for this is a little different as the problem only occurs Torrent based. NZBGet already removes the sample/sfv/nfo stuff based on what I have setup in NZBGet.
For me, when it finds a Torrent, it drops does:
Sonarr - Finds a torrent -> Blackhole
Blackhole->BTSync->Seedbox
Seedbox finishes torrent->BTSync->Sonarr
Cronjon on Sonarr boxes runs NzbToNzbDrone and that processes the ‘done’ btsync folder as NzbToNzbMedia handles any RAR or ignores btsync file.
I also have remove on as well.