Yeah, I recall directory paths being the biggest PITA with running scripts in cygwin. But I mean, that was a very minor set of things to fix compared to what would've had to be written in anything else available at the time.
Doing retail office deployments of custom code on employee computers is a weird niche, and you find whatever works and hope you can maintain it somehow. Cygwin was awesome though, saved me a ton of time and the client a lot of money for the moment. (The client later stipulated to all future franchisees that they had to buy only Macs, lol)