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Putting HTML and JS in different files doesn't make them separated. They are still bound by logic. It's an imaginary separation with obscure dependencies. I very much prefer the React way of bundling things that in reality belong together.
It is quite possible to develop semantic, content focused HTML and then at a later point style and re-style with CSS. It is only through laziness and lack of understanding that people couple them together.
The separation that scales is the one that pairs a small piece of DOM (like a piece of text on the page that updates with the current stock price) to the JS that goes with it, and put that into a single file. Now, build your web page out of components instead.