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Thanks for asking.
The only way I see this possible is by
1) pairing an Apple Remote (or Apple Remote profile on your Harmony) with your Apple TV
2)
a) enabling support for multiple remotes at Prefs > Hardware > Built-In Receiver
b) add all the Apple Remotes you want to use with your Mac there, NOT adding the Apple Remote from step 1
c) assign the same logical "Apple Remote" to all remotes added there
d) follow the steps in http://www.iospirit.com/blog/article/131/Remote-Buddy-and-Boxee-Plex-and-XBMC/ for forwarding Apple Remote button presses to Plex
Best regards,
Felix Schwarz