one thing that struck me is that markers can't be zero-width. Well, they can but they won't show up. I'm wondering if this is related to the technique mentioned here

Thanks for bringing this up. It's not a fundamental limitation at all. Highlights whose markers are zero-width are deliberately filtered out here[1]. This might not be the right move. If you've found it inconvenient, would you mind opening an issue on atom/atom, and describing your use case?

[1] https://github.com/atom/atom/blob/ebc5758d79e421f61f2b6669a8...