It is annoying that the Nightly always overwrite the settings of the releases.
If you start to check a bugfix a nightly and then again the last release, all settings are gone.
settings.xml = Release
settings_n.xml = Nightly
If you upgrade Simutrans, there is no guarantee of being able to go back down. This also applies to save games. If you just want to test a version, it is perhaps best to install it as a single-directory installation. You need to copy the save game over, but since you need to copy the settings over anyway to ensure you test under the same conditions, that doesn't complicate things much.
I already use singleplayer since I use several releases.
And I would therefore otherwise always override the settings in the user directory.