Hmm, as I suspected the warnings cannot be ignored, as the build fails on cygwin without the autoreconf step (it spits out errors about incompatible autoconf).
If modifying those files is really a problem, what I can try is to let the build.sh script run configure + make, and if it fails, then try autoreconf + configure + make. This way, it would only effect a subset of people.
Another way would be to copy the whole source tree to build, and then only modify the copy.
Maybe the latter is the preferred approach?