Hi Louis,
This is slightly confused because you talk about RaPi -> Pixhawk -> PC and then you talk about PC -> RaPi via antenna/USB and so I don't know what configuration you are trying to achieve.
Also, what flight stack are you running on the Pixhawk?
What you want to do is probably possible, but I have not personally done it. The main thing to consider (assuming the first case) is routing between interfaces. So if you send a message from RaPi to pixhawk you need to make sure that:
1. The message is then forwarded to whatever interface you are using to connect Pixhawk to PC. ON some flight stacks this might be automatic while on others you might need to explicitly enable forwarding.
2. All systems have a system id and component id. Even if you are sending messages over a wire, the protocol expects you to specify a sender.
3. The custom message is understood by the routing system - Pixhawk. In theory a system should route a message it does not understand but in practice it may not.
4. The custom message is understood by the receiving system - QGC. QGC needs to know what to do with the message, so it must use a build that understands your dialect.
Regards
Hamish