@BorisBlagov Update: the plugin now implements exactly what you are looking for and renders [[note|$eq$]] correctly. It also works in live-preview mode.
You gave better instructions here than you did on your documentation site or your github for the plugin. I think you should copy and paste this whole interaction on your github. I’ve had this plugin for a week, and just happened across this post. It has examples with context.
It’s been a while since I have been here, but I want to thank you for that - exactly what I am looking for!