I last used Atlassian stuff about a decade ago.

Did they ever get around to fixing basic bugs like "Jira and Confluence use different markdown dialects"?

They've had a decade to address those sorts of obvious problems that bite 100% of the end users of their stuff, and apparently employed over 1600 people during that decade. That's 160 centuries of person time. I wonder what it was wasted on, if not making their fairly small core product suite usable.

I think we're going to see more and more incumbent companies with big moats and terrible products get replaced with vibe coded solutions over the next year or two.

No, they simplified it by cancelling almost all non-cloud instances and moved to being a direct per-seat SaaS, with (apparently) all the same bugs but fewer features.