It doesn't really matter anymore. It's been conventional wisdom for years to develop in a Linux VM if you have to use Windows otherwise. Unless that turns out to be more complex that the Windows Linux subsystem, I can't see VMs becoming an also-ran.
If a Linux VM is fine for deployment, well then that specific component doesn't really need or use Windows very much does it. (That all unixy things need to put in VMs on a host running Windows is a very different constraint.)
If it's important to deploy as a Windows process, then the Windows Linux subsystem is not much better than a VM. Point is, its no substitute for a (better) MSYS2/Cygwin.
I think I understand your point, and it's been a while since my MCSE expired, but unless Cygwin has improved a lot I would estimate a VM wrapped by Windows would be much easier to manage and admin.
Now if you're saying that the webapp itself would be required to be a Windows process, there's really no way around that. But as I implied elsewhere, the biggest stumbler for Rails on Windows has always been the lack of a compiler. Whether you compensate for that by installing a subsystem with that capability or by using a VM with the capability is largely a local problem to the company.
