PeerJ has actually quite a few publications, one of them is CS ;) https://peerj.com/computer-science/ the dropdown on the top left allows you to switch between them.

I think MathJax is certainly a step in the right direction, they even support rendering to MathML.

But I agree that there is a certain lack there in terms of full semantic representations. MathJax is more accessible than TeX but it's still describing visual layout, instead of semantic meaning.

Pushing HTML to arxiv is also a step into the right direction.

I think the most important thing we can do is not be complacent with the state of the art. We need to go back to an age of computing where we didn't think we had it all figured out. We need to experiment, and not be afraid to take a step back in some aspects, like layout and kerning, in exchange for other advances like semantic representations and knowledge representation.

I think bred victor has a great talk on this: https://www.youtube.com/watch?v=8pTEmbeENF4

I think we need to experiment with things like observablehq.com or nextjournal.com or the many other that are coming into existence.