Hi @vpelizza,
You’ll be interested to know that Jira Server is moving to a new look and feel more in keeping with the ADG: Coming soon: Updated look and feel for Jira Server. Confluence Server and Bitbucket Server are also adopting this aesthetic as well.
You’ll also be interested to know that the AUI project is re-implementing its styles to more closely match ADG3. Take a look at the progress here: Upgrade guides - AUI Documentation
As for making Atlaskit look like AUI / the current design in Server products, my advice would be to not worry about it. Why is matching the host product’s design important to your business? Is it the most important aspect of your business?
If you adopt a long term outlook, the design systems will align over time, so your app will “fit” in a Server product regardless of whether you’re using AUI or Atlaskit. Yes, for the current versions of Server products, there would be some aesthetic difference – but your end-users probably either won’t notice or won’t care 
Hope that helps.
Cheers,
Daz