I think this goes deeper. Transparency is clearly not a good fit for desktop or mobile apps, but imagine smart glasses where every app completely blocks your view of the things behind it. It just wouldn't work.
To move around safely with smart glasses on your face, apps need to be semi transparent from day one. It's not about superficial stylistic similarities this time. And it's not primarily about design either.
This is absolutely about core usability, just not for macOS or iOS.
You seem to have a more solid idea than I of what a Vison-like device is for. As far as I know, it’s for approximately nothing. I have no opinion on what I’d use a $4,000 AR goggles for besides the world’s most expensive way to watch Netflix on a plane, or the second-most-expensive monitor you can buy for your Mac (Apple’s hilarious $6K 6K monitor being the first, of course).
So I don’t think I necessarily buy that apps have to have any transparency at all. If I’m walking around doing things in the real world with a Vision Pro on my head, that itself beggars belief to me. It’s wildly impractical for that with its 2-hour battery life, super heavy weight, and hilarious appearance, and all those will continue to be true long after the 5-year window when the “26” OS aesthetic will likely persist.
So, might some future glasses or something benefit from transparency? Maybe. But if I find myself walking down the street with a screen on my face, I’d personally prefer to just close the apps that I don’t need, rather than look through them. If the glasses are going to highlight place names, people’s names, etc. they can do that with text floating in midair, like a subtitle.