All this is doing is using PUTTY as a serial console rather than its more usual use for SSH.
You can use any tool that is capable of listening to a virtual serial port. PowerShell, Node.JS or Python for example each have libraries to do this. Or any of the "old fashioned" terminal tools we used to use when connecting over modems to Bulletin Boards. :) Hyperterminal is available on some versions of Windows.
All you are doing is giving the software the address of the pipe instead of the more normal COMx: address.
Not sure but I would think you could reference the pipe from Cygwin but that just seems a little over-complex. Minicom or screen would be the normal tools to use on a Linux box.