@sfg The baseUrl field will continue to refer to the xxx.atlassian.net site URL and will not reflect any custom domains applied to a site. This is the URL you should use for any REST API calls. The same will apply to the ACE framework.
For rendering links, serverside, you should use the new displayUrl field when it becomes available. We’ve delayed the rollout of the new fields as discussed in ETA for custom domain lifecycle payload changes - #13 by tbatagiannis