There’s actually a hidden feature called Application Templates that allows you to do this:
Application Templates — Blender Manual
Once you get it set up it’s pretty easy, but I actually don’t go this route. Since everything I record is the latest stable version of Blender, that is my vanilla version. I use Blender Launcher to keep on top of daily builds, and those are what I have all my custom preferences set in. Once a new version is released and becomes stable, I carry over my custom preferences to the next beta and then load factory settings in the stable version like Spikey mentioned.
That just happens to work well for me, but the application templates is probably your best bet.
