Today, you query your users from your database. What if you decided to delegate the authentication to an authorization server? I've seen this happen before: people decide to create a Web API to deal with authentication/authorization details. If you were using the DbContext directly, you would have to change everywhere you would be using it.
By using UserManager on the other hand, you would just have to change the implementation of your UserManager to use an HttpClient, to consume a Web API in order to query users, roles and other stuff needed to create your user Identity.
The UserManager encapsulates the implementation details through the IUserStore and some other interfaces. I'd avoid querying any of the Identity tables directly, even though it's very tentative.