It seems any conditions in makes dont work. And addprefix too... make say that addprefix is not exists. All makefiles from atmel examples. And all example makefiles have conditional statements.
Try make version 3.81 first, it there are still problems create a minimal example so the issue can be reproduced.
I tried make 3.81. It has the same problem.
I tried old 3.75 version and some example has been compiled