Agreed. I guess what make tickles my brain about it is that you can have a rather complex set of automation, integration etc. under the hood, while keeping the surface somewhat clean.
While you do have some valid points, especially when it comes to friction between PM/Devs, the way you seem to be using Jira seems to be the polar opposite of what I have experienced.
Granted, I don't have an overwhelming amount of experience working at different companies, but I feel like the Devs in my company were actually the ones that wanted to use Jira for customization options.