I would say that the author is onto something here. There is obviously pain present. I have used Jira in various weird scenarios, most recently I have created a setup for accounting operations to track client work and repetitive tasks with some automation also. It forced Jira a little bit but at the end people are using it and appreciating it. The thing is that you just need to spend some time thinking about it from the user perspective. Having something flexible with unrestricted hierarchy and smart linking with some possibility of automation would be grand.