> No, w32-pass-lwindow-to-system that running emacs from the command line
and in emacs with "emacs -Q", both are t.

Ok. You're sending low-res images, which are hard to see (at least to my
old eyes), and in one of a few hours ago I thought you were showing
w32-pass-lwindow-to-system, while in fact it was w32-lwindow-modifier. I
got sidetracked by that mistake.

So, to summarize (again), if you run

 emacs -Q

from that 2019-09-18 snapshot,  then in that running instance,

 - w32-pass-lwindow-to-system is t
 - w32-lwindow-modifier is nil,
 - and lwindow+r does not invoke Windows' Run command.

while it does in my setup. Weird.