<lwindow> is passed to windows system in emacs 26.2 with the same init file and packages.
------------------ ???????? ------------------
??????: "Juanma Barranquero"<lekktu@gmail.com>;
????????: 2019??9??25??(??????) ????8:44
??????: "Albert"<georgealbert@qq.com>;
????: "Eli Zaretskii"<eliz@gnu.org>;"37495"<37495@debbugs.gnu.org>;
????: Re: bug#37495: 27.0.50; lwindow doesn't pass to system
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)"