I do a similar thing where the agent runs in a Docker container and I talk to it with Telegram. It has GitHub CLI access but only with a very restricted PAT. No bind mounts. Jira is pretty clever, though I'm not feeling enough pain with just Telegram to want to try switching at this point.
I have multiple relatively well-established Jira projects I've been able to add agents to, and also clone/use as a template for new agent-only projects which give me another kanban to manage, pretty comfortably ..
The big thing about my Jira use besides the fact that its a historical tool into which I've integrated agents, is that managing agents through Jira's custom workflows is really, really cool. You can actually do any of the old workflows with agents - they'll just do it. Finally, effective waterfall! ;) *Just kidding, I've always been able to do waterfall properly...