You should be able to control Plex with your Apple Remote when not in Universal Mode (which is a special mode for a special Harmony profile that emulates several different Apple Remotes). That this doesn't work is a strong indicator that something in Plex itself is not working correctly on your system.

PlexHelper does the same thing as Remote Buddy does for Plex: it converts button input to UDP packets it then sends to Plex. The contents of these UDP packets differs depending on whether you're using Plex' Universal Mode or the Normal mode. If Plex doesn't react to the Normal-mode UDP packets sent by its own PlexHelper (which is used when you don't run Remote Buddy), then Plex will also not react to the same UDP packets coming from Remote Buddy. This, however, is not an issue of Remote Buddy - and can also not be addressed by Remote Buddy.

However, once you solve the Plex issue and Plex does react to the UDP packets coming from its own PlexHelper again, it should also react to the same UDP packets coming from Remote Buddy again.

So step 1 to the solution (and probably the only step) is to solve the issue your Plex installation is having with Normal-mode Apple Remote support. For this, as I said previously, please contact the Plex team for support with identifying and resolving this issue of Plex itself. I really can't help with that.

Best regards, 
Felix Schwarz