Just a comment: apart from the "Remove annotation" option, one can also undo highlighting by selecting text, then hitting Ctrl+Shift+K. (Just like Ctrl+K adds default highlighting.)
But yes, having Ctrl+Z available would be nice. Even more important IMO is having the highlighting function available in footnotes.

I strongly agree. Logos resources are increasingly taking the place of our physical libraries. I am very happy for my kids to raid my bookshelves, and in the same way I'd love to be able to have them use my Logos library. But they should have their own username, so they could add their own layouts, highlights, notes etc.

thanks! this is very helpful.