Greg,
Abstracting the base library is an optional part of the design. I'll leave it up to you to decide if it makes sense for your application. In my case I've elected not to abstract the base library and I use jQuery, underscore, etc. directly in core, the hub and modules. The problem with this is a dependency is created between my app and the base libraries I am using. The advantage is that I don't have to invest in abstractions that I may not need. You'll need to weigh the cost of abstracting the base library, which can be quite high depending on the complexity of widgets your app uses, against the benefit of being able to swap out that base library at any given time. Because the projects I work on are ok with a commitment to jQuery this abstraction represented a much larger cost than benefit.
There is no one right way to go about it, but yes, abstracting the base library is the most flexible approach. If flexibility for switching base libraries is a requirement for your application then you should abstract them.
Alan