My organization uses all of Atlassians products. Every time I as for a sane alternative and get shot down I question whether I want to work here.

Can you recommend a replacement for Jira that can be self-hosted? Many companies cannot store their data on a third-party server.

Take a look at Gemini[0] for self-hosted issue management and help desk ticketing.

[0] https://www.countersoft.com

There's at least Redmine. Uses Textile by default, but there were plugins for Markdown.

Redmine nowadays also comes by default with Markdown.

Menu Administration -> Settings -> General tab

There's a drop down for Text formatting which you can set to Markdown.