I wouldn’t worry about waveform, thumbnail, and autosave. The first two will rebuild automatically very quickly, and AS is small enough you wouldn’t need to dump those.
As far as Scratch, if you set one main destination for everything, FCP will automatically create a new folder with your project’s name. You can then save this folder to whatever drive you choose when archiving. And, if you need to revisit the project, you can quickly reconnect your media to the new location…should only take a minute to do so.