There's some special handling when loading the image where it does different things depending on the value of the subsystem field, but I don't know whether there's any special handling in the kernel that can't be duplicated by using the native api. But the NT kernel does very little when it comes to initializing new processes, most of the initialization is done in user space by ntdll, so it seems unlikely.
> had problems with getting it to work with the win32 subsystem
Keep in mind that the whole _point_ of Cygwin is to interact with the Windows world. If you want a POSIX sandbox, you can use a VM with fewer headaches and better performance.
Anyways the cygwin guys claim to have forked processes with ZwCreateProcess, but just had problems with getting it to work with the win32 subsystem: http://www.cygwin.com/ml/cygwin-developers/2011-04/msg00034....
Also this guy seems to have managed to do it: http://stackoverflow.com/questions/10657699/cant-use-createp..., but it hang when he called a win32 function (CreateProcess) from the child.