[jasomill]

On your own system, sure.

As a dependency of a shipping Windows application that needs to cleanly coexist side-by-side with existing Cygwin installations and optionally support silent install/upgrade/uninstall through mechanisms like SCCM, Intune, and Group Policy?

Not so much.

I do use the setup program to build the self-contained Cygwin root that's ultimately bundled into my program's MSI package and installed as a subdirectory of its Program Files directory, however.