In my system, using that very same snapshot, w32-pass-lwindow-to-system is t and it doesn't swallow any LWin command.

So it seems something specific to your setup.

What does

emacs -Q --batch --eval "(princ w32-pass-lwindow-to-system)"

return?

Does it change if you do create an empty directory, let's call it C:\EMPTY, and you set HOME to it?

set HOME=C:\EMPTY

emacs -Q --batch --eval "(princ w32-pass-lwindow-to-system)"