there is no default GTK theme on Windows
There is, its the same default everywhere, the Adwaita theme that everybody is complaining about, but exactly where its located I'm not sure, somewhere inside GTK, possibly in an internal form, not in a CSS. So it will get "upgraded" when Geany is because GTK is included in the Geany install. Technically a theme you install is applied as an override to Adwaita, although many downloadable themes seem to override _everything_ :grin:
copied it in C:\Users%USERNAME%\AppData\Local\gtk-3.0
Only the `settings.ini` goes there, the themes go in `Local/themes` according to the FAQ, but clearly either works. But still if you upgrade the theme, for example if it fixes issues, it will overwrite your edited one, hence my suggestion to add changes to `geany.css`. Although GTK CSS is not complete Web CSS it works the same way, the most recent matching rule will apply, and as `geany.css` is loaded after the system theme anything in it will override the system if it matches.