/copy_reference/save returns [409] no_write_permission

Regarding the 'no_write_permission' error, I suggest opening an API ticket with the full details of the API call you're making so we can look into that more specifically for you. Please redact just the access token.

Yes, you can use the /2/users/features/get_values user endpoint to check which features a particular account currently has. Please refer to the Team Files Guide and this blog post for more information.

And no, it's not possible to configure a different default root, but I'll pass this along as a feature request. I can't promise if or when that might be implemented though.