Almost right. I tested this on my computer and the result was that enabling that rule will ignore scanning when the server is adding things to the library/fetching metadata and artwork, but also will ignore the browser instance of the Plex Web App that will actually play the episode.
Eg: Downloaded DanMachi which got picked up by Plex and scanned into the library. HAPU marked this episode as watched.
Enabled the "Plex Media Server" rule fixed this problem. Opening the Plex Web App (http://plex.tv/web/app) to play Fate Stay Night UBW got ignored. Disabling the rule let HAPU see the streaming.