I am absolutely going to try this.

One question. Is there any way that if I click a JIRA link somewhere, like email or Slack, that it could open in the TUI instead of in the browser? I just can’t imagine that being possible.

Its possible- you'd have to register a new uri handler to call the TUI (it'll need to take cli args to load the link/issue), then rewrite Jira links (tampermonkey script/browser extension) to use the new uri.