You can define the environment variable FG_HOME to fit your needs: Windows system preferences -> search "environment variables" -> add "FG_HOME" with a value "D:\FlightGearHome". Do not use the same directory than the installation directory, do not use spaces just in case.
Source code where this is defined:
https://sourceforge.net/p/flightgear/fl ... t.cxx#l466 The default value is a few lines about this one. For windows: SGPath::fromEnv("APPDATA") / "flightgear.org"
EDIT: oh, sorry:
"C:\Users\youruser\FlitghGear" is not FG_HOME. You can find FG_HOME in "C:\Users\youruser\AppData\Roaming\flightgear.org", which is by default a hidden directory in Windows. FG_HOME is used for configuration and caches.
"C:\Users\youruser\FlitghGear" is the default directory for automatic downloads and your custom scenery and aircraft.
- You can change the downloads directory in the launcher: "settings -> downloads". This works for automatic scenery and aircraft.
- I'm not sure if you can
prevent the creation of "C:\Users\youruser\FlitghGear\Custom scenery", but this directory is intended to be used manually. If you don't use that directory for your custom scenery, it will be always empty. The same goes for "custom aircraft"