I have exactly the same issue - 1x NFR24l01 Transceiver on the Yuns SPI pins (ICSP header).
Tried for ages to and everything to get it working.
I have tried your code it shows this error. But magically cleared the problem and starts the SPI working with the NRF ? - No idea My full Post here:-
https://forum.arduino.cc/index.php?topic=430189.msg3107960#msg3107960
Maybe someone knows what to do to fix it.? For now I've ran this in the .rc file as a startup Bash to try clear the issue. Feels like a "brush under the carpet fix" but hey.
root@arduinoyun:~# reset-mcu2
ash: write error: Device or resource busy
/usr/bin/reset-mcu2: line 3: can't create /sys/class/gpio/gpio21/direction: nonexistent directory
ash: write error: Invalid argument