As promised, I tested the gpio. I2c is fine but there is a problem with spi. Default, cs pin is not working. This is how I changed the overlay file. It works flawlessly.
Okey I understand, in sun50iw6.conf
if [[ $BUILD_DESKTOP == yes && $BOARD == orangepi3-lts ]];
I always build server. I will try desktop build.
And after you update your repo I will test it again.