@Nca78 Yes, that should have been clear to me by now.

I just lost some time trying to burn the boot loader as always I got this error:

avrdude: stk500_getparm(): (a) protocol error

Checked, tested and even redid the soldering to exclude any wiring problems. Turns out adding a cap (0.1 µF in my case) between the programmers GND and RST did the trick.

Thank you all!

@gunther After fighting with this problem for some days, I now got it working. The solution was to use the BCM driver instead of SPIDEV.

I achieved that by commenting out the 32 bit gcc flags in ./configure

function gcc_cpu_flags {
    local soc=$1
    case $soc in
    BCM2835)
        flags="-march=armv6zk -mtune=arm1176jzf-s -mfpu=vfp -mfloat-abi=hard"
        ;;
    BCM2836)
        flags="-march=armv7-a -mtune=cortex-a7 -mfpu=neon-vfpv4 -mfloat-abi=hard"
        ;;
    BCM2837)
        flags=""
        #flags="-march=armv8-a+crc -mtune=cortex-a53 -mfpu=neon-fp-armv8 -mfloat-abi=hard"
        ;;

and running configure with this options:

$ ./configure --my-transport=nrf24 --my-gateway=ethernet --my-port=5003 --soc=BCM2837

Hope this shortens the learning curve for 64bit Rasperry Pi users!