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Thanks for asking.
If you use the actions supplied by the Remote Buddy Plex Behaviour (as is the default), these are turned into UDP packets and sent straight to Plex. These don't go through PlexHelper.
If you use the actions supplied by the Remote Buddy Virtual Remote, these are turned into Apple Remote button press events that whatever application currently has a lock on the receiver will receive. For Plex, that 'll typically be PlexHelper. You can use Remote Control Diagnostics from the Labs section to find out which application currently has, if needed.
For questions on options, functionality and bugs of Plex and PlexHelper, please contact the Plex team directly. I can't help you with these.
Best regards,
Felix Schwarz