Not really. Opinionated software is good when the opinion is something you agree with. When you need the opinionated software to something it wasn't designed for it's frequently really bad.

CMake is opinionated. It's built assuming that the build yields an executable file for Windows, Linux or Mac. Try getting CMake to cross-compile for more than one platform at the same time, or build not than one executable and then build a root filesystem into a system image. This is impossible without circumventing CMake entirely. It's actually pretty easy in Make, which is what CMake generates.

There are tons of organizations which need to manage their projects in a way Trello or Pivotal aren't designed for. These tools require you to adopt a methodology and they work great as long as you do. But if you need to do something strange like integrate with a separate system test team, good luck. That's really why organizations adopt JIRA. They want to do things that the tool designers thought you should never do. And those things are necessary in the eyes of those organizations.

Being opinionated is great if you're a human, but the best software is built by people who are trying to help me do my job, not by people who want to dictate how it should be done from the perspective of not being my employer.

Everything you state as being a "benefit" of Jira's customizability is why devs hate it. The software's features aren't being used to help developers do their jobs, which was the original reason for the product, but to help managers and report fetishists collect reams of unnecessary data points. It is a hindrance to your organization, but at least you get to make sure all those checkboxes are checked.

It sounds like you're either one of the report generators, so it's awesome for you, but all your devs hate it.

Probably the source of almost all of their sales too.

Sane defaults are good, customisation for those that want it are also good. A single way of doing things, good for those it works for.