At PyBay last year, I ended up with a knot of Python core devs talking about this problem, and talking about building a better, more portable API for native modules. The transition would be nasty (the 2->3 transition was..scarring), but it would solve this problem at a stroke.
> I very much prefer Python over JavaScript for example, but even then it wouldn't cross my mind
I would encourage you to at least check out Anvil (https://anvil.works). It's more than a Python->JS compiler; it's a reimagining of what the web as a platform could look like.
FWIW, I agree with you that it's a bad idea to swap out JS for Python at one layer, while keeping the rest of the stack intact. It's extra complexity, and it doesn't solve the actual problem with the Web, which is the sprawling complexity of the stack and all the weird frameworks that work around it (while themselves making the problem worse).
The Big Idea of Anvil is to replace all those different layers of abstraction with one big, coherent abstraction. That's one reason why we deliberately chose Python rather than JS, so that users wouldn't reflexively reach out and break that abstraction every time they Googled how to do something.