What I do is I create an empty project template that has every possible preset I could use, including Auto-Save timings, Keyboard shortcuts, clip settings, color science, reference clips, PowerGrades, the whole thing.
When I begin a new project, I just open one of the saved templates, do a Save-As with the new project name, and go to work. No muss, no fuss, no surprises.
You can also save most (but not all) of this stuff with Project Settings -> Presets, which are covered in the manual. Keyboard Mapping would definitely be saved there.