We have new version of the WiringPi will release next week. About the GPIOs, many of them are reuse, may configured as other other fucntion (I2S, SPDIF, I2C…), if you want to use them as GPIO you need to modify the DTS.
Wi-Fi (AP6398S) is a known issue in mainline kernel, but have some good news now.
The should be the same.
Are you sure about this ? The FAN mode is auto by default. It should be work. You can also edit /boot/env.txt to change the FAN mode.