Well, modifications of GTK theming affects Inkscape, and possibly other GTK apps. Looks like GTK is not designed for Windows. This was interesting experience. I propose to the Geany Windows maintainer to keep Adwaita as the default theme. If I do not like the default theme of next versions, I will compile Geany myself with another theme and use that. Can't mess up visuals of all GTK apps on the machine.
See https://github.com/geany/geany/issues/3063#issuecomment-1009446219 - you can have per-application themes and Geany definitely shouldn't modify the shared `settings.ini` common for all GTK apps. This also means that Geany can use a theme that suits best to its use of GTK widgets and this theme doesn't necessarily have to look good in other applications.