To answer my own question, and to hopefully help others in the future...

I missed the part about creating a Telnet login for the Crestron processor in the main repeater. This required extracting the Ra2 program (which we didn't write), making the new login and then uploading it back into the main repeater. We then used those credentials when adding the main repeater to the Crestron Home processor (MC4-R in this case), and after that, it allowed the button presses to actually function.

It is pretty misleading, though, allowing it to add the main repeater, extract the data and even create the buttons on the interface without allowing it to work. I called Crestron tech about it and they didn't know how to help, and their huge Crestron Home document made no mention of it as well. A little disappointing, that one.