It's very easy to set up different defaults for the start-up scene. First create a scene exactly how you want the default to be, including all settings and nodes. Then save it as a TGD (File -> Save As) in a location that will be easy to remember. You might want to name it "default scene.tgd" or something similar. Now go to the Preferences (Edit -> Preferences) and in the first section "Startup", on the right you'll see the "Project Creation" option which will be set to "Use defaults". Simply use the drop-down menu to select Load From File then click the Choose File button, find your file and select it. OK out of the dialog and the next time you start TG2 it should use your custom startup settings.
As for why the 3D preview buttons "disable themselves", they are actually tied to the Layout View you are in, e.g. by default the Terrain layout will disable atmosphere and lighting because it is assumed that these may be less necessary for viewing your work on the Terrain (and may even be a hindrance) and are therefore turned off to increase preview render speed. In a given TG2 session, whatever you change in the 3D preview on a given layout will be remembered when you come back to it. There is currently no way to change the default per-layout 3D preview settings as far as I know (this may be saved in TGD files but I don't think so).
- Oshyan