The current era really overestimates the benefit of using third-party cookie cutter tools. Yes they save on development cost of course. But you're stuck with something that has a million complexities you don't need and that is mostly terrible for everyone. So you pay in an infinite stream of small annoyances which add up.
There's a lot of value in building in-house tools targeted to work exactly like your team works with zero extra complexity.
And look at all the years-and-years-and-years-old jira feature requests that atlassian never bothers to implement and you have to suffer with mediocre workarounds. With an in-house tool you change it in an afternoon to do exactly what you need.
It's not for every company but companies of enough size to support building in-house tools should really give it more consideration.
I used to work in a largish public company (40K+ people). They had a wonderfully functional and flexible bug tracking system.
So no, at least in my experience one can be in a large org and enjoy your bug tracking tool, nothing to do with the overhead of a large org.
But jira, it is beyond awful.