If you

a) start with the default settings and 
b) follow exactly what is written in the blog,

Apple Remote codes will

1) control Remote Buddy when Plex is not running (Plex Helper isn't 
relevant at this point, since it has no UI and thus can't be the 
foreground application).

2) be forwarded 1:1 to the OS (and thus Plex Helper) when Plex is 
running and in the foreground. What Plex / Plex Helper are making out 
of the Apple Remote codes is outside of Remote Buddy's control.

Please note that

a) only when Plex (not Plex Helper!) is running, will it receive Apple 
Remote codes in this configuration

b) tutorials/features/wiki articles that require Plex/Plex Helper to 
be the one, only and exclusive application to have access to the IR 
receiver will also only work if that is the case. Also, the 
requirement of exclusive access to the IR receiver and all events 
coming in from it all of the time by its very nature excludes the use 
of any other application with the IR receiver. If I understand your 
original posting correctly, the tutorial you were following does have 
this requirement, since the only way such a thing can work is by using 
a background application that requires to receive all events from the 
IR receiver.

c) you can start Plex through Remote Buddy's menu.

Best regards, 
Felix Schwarz