One of my ideas what to create Atlassian plugin that would allow to use custom domain.
I did some PoC. With heavy http proxing/rewriting it would be somehow doable but too fragile. I have skipped that.
Basically all of this is matter of Atlassian priority. If most of clients can accept current state then why bother?
It is good market, there are niche needs. Most of work is web development not rocket science.
Actually plugins for Jira / Confluence is something well done by Atlassian.
They can not create single solution for all, but with plugins? It is close.