deskthority

Uhm, what about connecting 2 MCUs (via UART or I²C)?
You can just define a hotkey in the matrix (or separate hardwired switch) to send the data from "master" MCU to ether its own USB or to slave MCU.

I don't know anything about RF PCB design, but I am guessing it could make problems.
Thre are some projects to look at and good documentation from Nordic semi, your only problem is QFN.

On the other hand, I don't like the antenna part of the transceiver getting too close to some copper traces on ...

Well, you could desolder the pin header from transceiver board, put it on the back of your AVR board (with doublesided tape/glue) and connect with thin wire. Cheap and very easy to make, you only need some attention while soldering and/or use some thermal resistant tape.

Creating an individual ...

Got mine at Zoll today, in less than 5mins and paid only ~15€ (instead of 50€+)

Thanks for a great GB!

I think I'm going to build a new KB just for the set

Paid.