For me a strict requirement for this is that I can use a particular template and document class. Unfortunately I don't have any choice as to what the particular format is. It's not clear if Madoko makes this possible.
It would be nice if journals would accept Markdown, but frankly I don't expect that to happen anytime soon.
Perhaps it would be easier to go the other way -- to modify a Markdown parser to output a simple subset of Latex that can fit into most common academic templates.
As far as I know, a lot of the journals have their own automated build systems for the manuscripts to perfectly fit into their designs.
Nevertheless, I've also encountered PDF uploads. But even then, the PDF will be automatically checked for consistency.
[OTOH, I've seen claims many publishers already have a process for publishing Word submissions — something involving monks spending their lives typesetting everything from scratch? — and so when they do get a nice LaTeX, they throw the source out re-use the above process! Perhaps that was only about the bibliography though.]
I've seen some Springer (LNCS) submissions, and those definitely included the .tex source.
arXiv requires the source, mainly so they can re-compile them in the future with better tools [https://arxiv.org/help/faq/whytex]. Unusually, they make sources available for anyone to download.