Microsoft is going to ship a headless version of Windows Server:
[1] https://etrading.wordpress.com/2015/10/13/windows-containers...
IIRC starting with server 2012 or 2012 R2, all configuration and management functionality was exposed via powershell commandlets, as Server Core was the default installation type and server management was meant to be done via winRM/remote powershell sessions.
I guess the software you mention that depends on having a desktop will do some combination of not working and working poorly, but they aren't targeting legacy applications with it, they are fleshing out their cloud offering.