Hi,
I've installed the same combination last week and it works great. I've chosen AV1, V-Mem,HDMI A and PUC1. First of all, my dealer have to update the PUC Library with different devices, we've selected from a PUC library. A downloaded follows via PUC1 and a Serial interface from his service notebook. After selecting AV1 - V-Mem, I've got the option to choose the PUC-List and I selected Apple remote and after storing all the key inputs the ATV is working with the BEO4 as expected.
This will be the right way to get the functionality of an apple remote over BEO4.
Hope it helps
HeKoch