yep, facing same problem about FN keys on my asus GL552JX at 10.12.4
but i was installing ACPI debug kext also patching EC query from DSDT due make sure the variable are correct, magically the Brightness keys are working.
im not sure if debuging acpi can give some bad feedback or performance or anything else abnormal from my computer, so i remove them out.
waiting for solution of this epic
thank you verymuch.