So far as I can tell, they did have one common markup syntax for all applications... but then Confluence users wanted a WYSIWYG mode, so Confluence now uses an XML-based format internally, and Stash is a Git tool and 90% of the Git ecosystem loves Markdown, so Stash had to use it too...
Markdown embraces HTML, and so a WYSIWYG mode based around HTML is compatible with Markdown.
Markdown's weaknesses for table design, image insertion, and complex layouts is all handled by HTML and WYSIWYG tools that edit that directly.
That would have solved the Git scenario, and the Confluence scenario, whilst having a single highly predictable markup across all of their platforms.
The problem really stems not from these problems being addressed per product as if they existed independently of all other products. But that's a terrible approach, as few people buy just Confluence without JIRA or Stash, people buy Atlassian because a consistent suite should work better than many myriad tools that don't quite know how to interop. Atlassian's strength is the consistent and integrated approach, so the UX should be focused on strengthening that.
