I have no idea why you're claiming that a programs running in a unix emulator (e.g. cygwin) is running on Windows, or what your point you're trying to make in the process.

Since I use an editor that doesn't add "\r" to the line ends, I don't normally encounter this issue, but I've encountered it a few times, and am sensitized to look for it.

Indeed. Windows and unix use different line endings for text files. One must account for that when accessing a from the other system (be it via FTP, SMB or Cygwin).