If the OS theme can change it then `geany.css` should be able to change it, its "just" a matter of divining what selector to use. Unfortunately when the UI was created in Glade the widget names were left at the default so "treeview3", "treeview4", and "treeview5" are respectively the status, message, and compiler window contents. You could try those.
Changing the names now would break every use of them, in Geany, in Geany plugins, and in external plugins we can't see. Essentially nobody is brave enough :wink:.
The compiler colours are handled differently because Geany parses the messages to detect errors and warnings and sets colours for individual messages to match, so CSS cannot be used since it doesn't know which message is which, and named colours are provided for Geany to apply by code. But only the foreground colour is set that way.