Is Jira a UX disaster because of just that?
Or is it bad on top of that?
The product has a ton of permutations, as you said, which makes stuff like this happen: Customers who never in the world imagined public issue tracking, suddenly bit by a feature they didn’t even know existed. Conversely I’m sure there are shops, who love this feature, for whom the distinction between “Everyone” and “Open” was always obvious. I don’t envy the team building / supporting the product across all that; I don’t know how I’d do it.
But there are also endemic, continuously-poor design choices large and small. Unannounced and hard to disable major changes to the UI are the standard, and large. I’ll give you one example of the small: Recently, unannounced, the issue comment UI started auto-correcting the capitalization of Atlassian product names in the comment box. Type “JIRA”, get “Jira”. In my words in my issue tracker. (Yes, it was the js app, not the browser). It just always seems so user hostile.
Net net, to me it’s an aging hydra of a product with ongoing missteps. I’d take good design and limited features over what you get here, at least with out heavy investment and expertise.