It's kinda funny: the Windows NT kernel (and Executive, the actual native API) are a single-root object hierarchy where everything gets mounted - much like unix - only even moreso. Mutexes, Registry Keys, etc are all objects mounted in the root filesystem.
I guess everything old is new again. Microsoft used to have a server product called Services for Unix that replaced the built-in POSIX 1.0 subsystem with a legit Unix environment but it was always a neglected product that only existed to get people to port server apps to Windows. This time they're doing the integration on end-user desktops and have spent more time getting Win API integration working smoothly.
Although it would seem logical, the WSL doesn't actually use this system. The whole pico process engine and how it interacts with Windows is all new and not related to that design. I'm not really sure the reasoning behind it; perhaps it didn't allow them to do the level of integration they wanted.
Everything else in the WSL is the regular Ubuntu user land. So all the processes are "native" and they make calls to a kernel that acts just like Linux.