This isn't a real answer because as far as I know there's no tool that helps you with this, but you should be able to put base-64 encoded images into markdown documents too. At the very least by just putting raw HTML image tags.

What would be "nicer" would be if one could use the references feature that allows you to put links in the body but their destinations in the footer to stash the images at the bottom of the document, but I don't think that'll work, and I haven't tried it.

That having been said, I personally think a folder of files, with images separated from the text, and referenced with relative paths, is better for 100 other reasons, with the only disadvantage being that you'd have to zip it up to send it to someone else. But if you've got embedding as a requirement, you could maybe try jamming them into the markdown.

Or make a new format! Mdgz, which is just a gziped tar of a file called index.md, and then a collection of any other files desired, and then get readers to resolve links only ever within that structure so it's encapsulated. Should be pretty doable, easy to work with if you don't have any special tools, but also possible to make tools for. I believe in you!