Is this something that used to work? If so, I probably broke it in bug 1256033. Though I don't see how the Makefile would have been picking up those dependencies prior to the moz.build port.
I'm not sure whether it is a regression... But I agree that it doesn't seeem to me changes in bug 1256033 could cause this. I guess we don't have proper dependency generation for host programs since some earlier days.