As a Windows outsider, I'm puzzled why programs used as part of the Chrome build system (which I'd expect to only use console I/O) are using APIs that cause interactions with the GUI? By analogy, is this not like gcc redundantly setting up a connection to the Xserver each time it is run?
(I'm making an assumption that NtGdiCloseProcess is part of the GUI API (GDI == Graphics Device Interface) which is why it may interact with the GUI message passing.)
In the very early days of NT the GDI subsystem was in userland and you wouldn't have this problem. Unfortunately it was too slow for machines of the 90s and so GDI+user32 is very tightly integrated with the kernel.
Even to the point where it does neat things like callback user mode code from the kernel. Unwinding this without breaking things is nigh impossible at this point.
(I'm making an assumption that NtGdiCloseProcess is part of the GUI API (GDI == Graphics Device Interface) which is why it may interact with the GUI message passing.)