OpenTX may run on an ATmega2560 processor in some of the RC transmitters that it supports but it is not an Arduino sketch. You say that you don't want to build the "companion" app but the companion app is needed to upload the new firmware to the transmitter. It might be easier to set up a small Linux system and use that to build everything. Linux tends to be better for automating tool installation and build processes.
For general ATmega2560 programming you might find better help at http://www.avrfreaks.net/.
Perhaps http://www.open-tx.org/ has information that would help.