You COULD probably overwrite e.g the preview render preset with a custom one, but I wouldn't recommend it. It's better to have some user settings to open for final output.

Also, you can make a default scene were the settings are included. Vue Infinite lets you make such a scene, that opens as the startup scene.
The lower versions don't have that feature, but you can get it with a little extra work. Just uncheck "Create empty scene on startup", and load your own "Default scene" as the first thing (unless you want another). I have Complete, and use this method. I've also replaced the default atmosphere with my own.

About the C3D items, I've deleted the ~~ files, as Bruno suggests.