I think this part of what you shared is interesting to discuss.
According to this article:
it is an ATmega128RFA
It looks like they did some cool explorations of this device!
You can add support to the Arduino IDE for the ATmega128RFA. There is a tutorial from SparkFun for it here:
https://learn.sparkfun.com/tutorials/atmega128rfa1-dev-board-hookup-guide#arduino-compatibility
I also suspect that the more popular MegaCore could be used, since the microcontroller in the ATmega128RFA is an ATmega128.
This is not a matter of whether a microcontroller is using "the Arduino firmware". It's simply a matter of adding the necessary support files to the Arduino IDE installation. Arduino only provides support for the popular entry level boards like the Uno in a fresh installation of the Arduino IDE, but they also provide the capability to add support for additional boards and microcontrollers, and between the other official Arduino boards and the ones created by the community, there is a huge selection available, and more all the time!
It's not clear to me what you mean by "the Arduino firmware". Perhaps you are referring to the bootloader?
You can do that via the Arduino IDE also if you like. Just connect the programmer to the board select the correct programmer from the Tools > Programmer menu and then Sketch > Upload using Programmer.