Geany uses a normal GTK toolbar and sets the [`primary-toolbar`](https://developer.gnome.org/gtk3/stable/GtkStyleContext.html#GTK-STYLE-CLASS...) class on it, as expected for main toolbars. The theme is then responsible for styling it as it sees fit.
I'm not very surprised a theme would style the toolbar (and menubar) dark, as many themes do it. I don't think this is a bug in Geany; but please make sure Geany is the only GTK3 application with a toolbar that is styled this way: if it's the case, we might need to further track this down.