Geany supports both GTK2 and GTK3, but the selection has to be made at compile time since thats the way GTK works. No application can be compiled with both at the same time. Therefore it cannot be a runtime selection between GTK2 and GTK3.
GTK2 does not read GTK3 themes and GTK3 does not read GTK2 themes so having compiled Geany with either GTK2 or GTK3 you are stuck with their respective themes.
The choice of what version to put in its repositories is the distributions, not Geanys. Ditto the choice of what themes to provide for GTK2 and GTK3.
Your only option is to compile your own GTK2 version of Geany and Geany-plugins or your own GTK3 theme. You can put your own geany.css in the config directory so it only affects Geany.