I agree with that, JIRA is so monstrously difficult. But this kind of limited configuration might not be so bad. If it's kept selective, some configuration is well-loved by technical users, the vast majority of GitHub's visitors.
I think the default order would be used by anyone who doesn't care to configure it.
In some sub-tab of the User Settings panels, there could be a drag-and-drop sort list (like the one for sorting the "featured repositories" on the profile) to arrange the tabs in a different order, and a button to reset them to default.
Maybe one other setting I would add is "dark mode". The CSS is essentially already written in public Chrome browser extensions to "reskin" GitHub's UI. This is because customizing light/dark modes is gaining in popularity. It's a new macOS trend and in my experience surprisingly common in iOS apps too. Since about 70% developers trend towards dark IDEs, it makes sense to have.
Unlike JIRA, I don't think any of these settings should be at the forefront... you should just have sensible defaults and a way to customize it. GitHub Help articles are well-indexed on Google and anyone who wants to know how to change the color mode or tab order is only going to do it about once, so clicking through menus is a familiar and safer-feeling (as opposed to direct links to private UIs) UX, and it's the same as any other process like adding a SSH key, webhook, or app password.
I do think that GitHub's main user base is increasingly loving their customizability. VS Code and Atom gain a lot of traction for their total customizability and extensibility with plugins. I'm not at all suggesting GitHub go in that direction -- but, GitHub is more of a cloud-based software tool than a website. A little bit of customizability goes a long way with user satisfaction, at least to tech-enthusiastic users.
Just little feature flags would be incredibly handy. For example, default to ignoring whitespace in PR diffs (a feature otherwise only available if you know the URL trick, and can't be saved to user settings like your preferred diff layout).
It's the same amount of customizability as "how many emails do you want to display per page" in Gmail. It's enough personalization to be useful and done officially instead of through hacky, dangerous, frequently-breaking Chrome extensions to work around the things that impede productivity.