I've been building with the attached patch on Cygwin for a long time, mostly for aesthetic reasons. (My build logs would be full of stray ^M characters otherwise.) Out of curiosity, I just tried building without the patch, and the build failed because at least one ^M got into a file name:
checking for CLISP libdir... configure: error: missing modules.c clisp.h in '/home/kbrown/src/cygclisp/clisp-2.49-1.20170321hg15864.x86_64/build/"^Mlinkkit'
[Note: I typed a literal circumflex followed by M above so that the ^M would be visible.]
So the patch is actually necessary, not just for aesthetics.
this boils does to the question of whether cygwin is unix or dos. :-)