OK, there are no replies because the genuine file doesn't contain such garbage.
It seems the files were corrupted when reading from a real USB hard drive via a virtual USB port in VMware Server. I wonder why the cp -pr command pretended to copy properly and the resulting copies were 99% correct. The other 1% contains garbage like trying to make checutil_sig a target, but the correct file doesn't do that. The number of lines in Makefile.in is correct, the number of bytes is wrong, and it's readable but 1% wrong.
I would expect this kind of failure to be more noticeable.
Maybe VMware Server is telling me to migrate to Virtual Box.