Jira is a workflow tool, which also means that most of the issues mentioned here, can be sorted out between the PM and devs on who the workflow should be, and what the rituals for updates should/could be. Jira is flexible enough to accomodate it (mostly). From a developer perspective, some of the points maybe valid, but not from PM perspective.
It would also help if we could get an idea of what the alternatives are, that are better
Edit: Also looks like marketing for the product, than a valid article on Jira pitfalls.