I think you give latex more credit than it deserves. It gives little straightforward control over layout and the only reason documents are manageable is that pages are fixed size and layout changes are mostly local.

It’s paragraph breaking was state of the art when it was new but other systems break paragraphs now and potentially better. I also think ragged margins aren’t really a problem.

I think if layout mattered as much as you imply, scientists would have to use a tool that offers more control like indesign.

None of this is to say that getting good layout in HTML is easy, of course.