You would have to modify Geany to use that distributed copy as the default when it creates a new config directory. IIUC currently it writes out defaults stored in the code.
Unless Geany is broken, it won't clobber the user's custom `keybindings.conf` file with hard-coded defaults, so if the MacOS launcher script puts some platform-specific `keybindings.conf` file in the user's config directory if it doesn't yet exist, Geany won't clobber it and instead use it as the defaults.