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The value depends entirely on specific conventions, but you've mentioned none. There is also value in consistent UI across platforms (which native UI don't support) as for some conventions you'd prefer to ignore the OS defaults.
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Not OP but I have a similar complaint.

The two primary OS items that turn me off of zed are not being able to have a title bar and the fact that menus open on hover and not on click.

VSCode, and IntelliJ let me turn on OS level title bars so I can handle the window without needing to try and find the magic spot not filled by some other app based nonsense as well as making it easier to see what window is active.

Menus can be unrolled from the hamburger but now pop open if I just swing my cursor through. I've no idea what convention that was pulled from but I think they just took the hamburger menu event triggers and left them as they were instead of changing them to act like an OS menu is expected to function.

I'm sure there are others that I'd find using the app but just those two was enough of a personal issue for me to just not bother.

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Good illustration - if you have a more ergonomic window management workflow that doesn't require hunting for a tiny bar at the top, have a custom more prominent active window indicator, and use keyboard to navigate menus, these are less of an issue.
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Unfortunately the reality nowadays seems to be that besides the dated QT, there are no good or popular cross-platform UI libraries for these use cases. It's bold that they built their own.
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Electron has basically killed this practice sadly. Which Microsoft modern app follows Windows native UI these days? Teams? Settings? Office? All dramatically different.
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TBH, Microsoft has made such a huge mess of UI on Windows, that even if you wanted to use the "native" UI you would have difficulties figuring out what that is, exactly, right now.

Having said that - Teams is a piece of #$%^&; and MS Office has dropped the ball with its UI switching to ribbons in 2007 and has languished in the land of bad UI ever since. Settings makes me want to just use Control Panel like a human being.

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You have, what, WinForms, WinUI, MAUI, and WPF for Windows currently. And that's not counting Win32 or Qt.
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And what cross platform code editor does that nowadays? vscode is electron, jetbrains has swing, ...
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Maybe what I'm saying is that people shouldn't use cross-platform UI solutions. (write-once-suck-everywhere)
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The old ones, and the ones that use Qt.
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If you are on macOS, there is https://nova.app/
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