Server product teams are exploring use of Atlaskit as their UI component library of choice when implementing new UI.
It’s likely that new stuff written in Server products will be in React and Atlaskit.
It’s up to each Server product team as to how rapidly (or even if) its existing UI will be re-written in React and Atlaskit.
Over time, AUI and Atlaskit will align in their aesthetics, so that it should not matter whether you have implemented your UI using AUI or Atlaskit, it should look like it belongs within the host product.
Using an approach like Dave’s for building Cloud+Server app UIs from a single codebase is a reasonable choice. Other vendors have chosen to take similar approaches, too.