That said, I'm loving the API design. Coming from Sublime Text, it's a massive upgrade. The ability to embed literally anything a web browser can render in a well-designed framework is mindblowing.
Thanks for bringing this up. It's not a fundamental limitation at all. Highlights whose markers are zero-width are deliberately filtered out here. 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?
Thanks in turn. :)