JIRA does this now.
Unless by JIRA does this now you mean, "JIRA allows for a many confusing setups, leading to the above situation more often than not" I have to disagree here.
What it doesn't do is require a workflow. It is possible to start with a Scrum wf, then progressively change it into a waterfall hyena with cumbersome required fields and impossible permission-based transitions. In fact, I've met many people who have the opinion that JIRA is cumbersome, just to discover that their sysadmin is a knee-jerk person who blocks any initiative within their entreprise using misconfigured software.
JIRA isn't opinionated in the sense of OP. OP suggests that saying "We use [Bug tracker name]" is equivalent to saying "We're Scrum with branch tracking and timetracking", because the bugtracker would enforce checks and a layout without much possible configuration.
For example, Trello or Bitbucket Issues are quite opinionated bugtrackers.
Then rely on the users being smart enough to not hang themselves with the rope given.
What you're talking about is, as you said, bad management. The reason opinionated software comes and goes, and JIRA stays is specifically because just like you can build sync on top of async, you can build opinionated on top of flexible, but not vice versa.