Going back to the original topic, I would also like to see something like what @cristian proposed. I don’t think using %%comments%% is the ideal solution because they do break up the text in live mode. Also, I feel like the block reference machinery is already almost there in terms of what would be needed for text annotation.
As comparison, this is how it works in Roam:
I created a reference to a block and then wrote comments under that reference. This makes a counter appear on the original block and when I click that, my comments appear in the original text under the block. This way, the comments are usually out of the way, but when I want to see them, they appear right under the thing I was commenting on.