Actually my .Xdefaults file *was* processed by perl/Tk even on Win32 (after I placed that file in $HOME), the point was it contained values that did not affected anything I saw.

When I put

*background: yellow
[download]

in there, it was obvious my file was processed

And while trying to solve my problem I've discovered an interest way to override .Xdefaults from command line:

perl -MTk -we "MainLoop(tkinit->Button(-text=>'test')->grid)" -- -xrm 
+*background:red -xrm *foreground:white
[download]

and really short GUI program without any punctuation:

perl -MTk -we "MainLoop tkinit"
[download]

Best wishes,
I.R.Baboon.