>I.e. I'm not sure the argument can be made that this is Atlasassian's fault.
As someone who spends a lot of his work life administering Jira and Confluence, I disagree. The problem is that these products try to be everything to everyone and as a result users have a massive degree of freedom with what to do and how to order things.
With that amount of freedom you just have a bunch of end users, many of them non-technical, who have no idea how they are SUPPOSED to use it. Especially because they don't want to spend a lot of time learning the right way to use the tools. They have a bunch of other things to do and just need to interact with this tool to complete their current task and then move on.
You are right, a sort of Wiki-Master would help. But, at least in my organization, we don't even have enough capacity to do all the basic administrative tasks required like setting up projects, workflows, custom fields, screens, etc. We can't also manage the content inside. The users are on their own in that regard.
If you are not willing to hire stuff with the sole purpose of managing the content of your Jira and Confluence instances, a more opiniated, rigid product is probably a lot better for your organization.