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/etc/rc.d/rc.sysinit regenerates /boot/kernel.h every time the machine reboots. This means that every time you run "gmake" in a kernel tree after a reboot, lots of files will be rebuilt because they depend on /boot/kernel.h (which is included by version.h), even though its content hasn't really changed. rc.sysinit should generate kernel.h in a temporary file, then compare it to the one that's already there; if it's different, it should replace the old one, but if it's the same, the temporary file should be removed and the old kernel.h should be left in place.
Fixed in initscripts-4.65-1, which will be in the next Raw Hide release.