Geany is a GTK application, so everything except the edit pane should "just work" and follow the GTK theme selected. Certainly here Geany follows the theme selected for the desktop as I change from Mint-Y to Mint-Y dark. And I don't even have to restart Geany. But note the desktop is actually selecting a different theme that somebody has created a CSS for, nothing happened automagically. If this is not happening for you maybe discuss it with your distro.

Unfortunately no desktop themes have styles for "compiler error", "compiler context", "compiler message", how remiss of them!!! So additional CSS needs to be supplied for those items, hence geany.css. Of course if someone contributes geany-dark.css and the method of selecting it a PR could be accepted.

The CSS also has no effect on the edit pane because that applies styles to lexical entities, and again no desktop themes have settings for those. So that will always have to have additional setup, hence the "colour scheme" for that.

Making dark/light colour schemes whilst ensuring appropriate visual contrast when there are many colours involved can be done in two ways:

manually creating dark schemes, several of which exist in Geany-themes and can be loaded and selected as you wish, or
inverting the colours in the selected theme, which is available with Edit->Preferences->Editor->Display->Invert syntax highlighting colours.

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