Keras is a wrapper around TF to make some common model operations easier (construction of linear layers of nets like a CNN) and to make common training operations easier.
So you can still do whatever with Keras by combining it with lower level TF operations, it's not really keeping you from doing anything. But more complex layer types and training might have to be rolled by hand, at which point it can be easier to just do it all at the lower level TF ops. This comes up a lot when implementing newer papers where they are proposing new training methods or Operations where you really need the flexibility to get in there and manipulate the ops directly.
