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Maybe there's a bug or some additional documentation needed on default library selection, but you can get something like what you want by deleting all of the contents of the files (after maybe saving a backup first) rather than deleting the files. It does seem to want to have those files all the time. That may be intentional, but the app seemed to work OK when I tried it just now.
Deleting the file contents is probably not a great idea, but the main reason I am answering is to say that I think you're conflating "model" and "library" here. The model itself doesn't necessarily include all those objects just because they are available in the app library. If you change the title/question to reflect that, you might get a better answer, and it is possible that there's a bug here.