So it is set by `Menu->View->Change Colour Scheme...`, which you can change while Geany is running, but not from the command line.
Well, you can't *readily*, but it's easy enough to either use a separate configuration directory (Geany's `-c` switch) or write a short `sed` command to alter the configuration before starting.
…Or possibly write a small plugin that would change the color scheme depending on the time, or some other global setting.