Scopes enable you to select more granular permissions; so we would recommend turning off any scopes your app does not require.
Single folder apps are rooted to a single folder, which is typically /Apps/(your app name). Moving to this structure means an app would no longer be able to see content outside this folder. This would likely break assumptions for existing apps (whose users may be accustomed to accessing content from another location), so we do not offer this option.
To move to an app folder, you can simply create a new Dropbox App. New users could use the new app, and you could have more control in helping users move to the new structure for upgrading users.