I vote for those being the default preference settings.
Enable loading of layouts from files and a "Save default Layout" action button that saves the file into the Users .Natron folder under a subfolder called Layouts and enables the correct file to load in the preferences. Maybe remember my last layout option is a useful desire as well.
Oh by the way it doesn't actually remember the scale size of the nodes nor does it seem to recall position of the view, if your default doesn't match the file already or you change it before opening the file with layout settings (hidden inside by default?).
The viewer zoom size should have an option to be permanently on center and remember it's to be Fit when selected to be so.