It simply slows everyone down, but when it's your only tool for tracking work, it's still better than nothing.
Now, the problem with Jira is not necessarily customizability but that it's dog slow, complex, integrations suck, and permissions system is chaotic. Still, I have yet to see fully customizable work tracking system that's better made than Jira.
But also, a fixed set of features does not force you to ascribe the same meaning to them like the authors intended: I've used "bug" tracking systems to manage large projects with great success (including big features, enhancements, but also big and small fixes).