Yay, glad it worked 
You could try setting .prodigy-content span, .prodigy-content mark { display: block } in the global_css. This will make each "token" and selection (in your case, the lines) a block element.
Just did a quick test locally and the selection and double-clicking still works as expected. If you also add something margin-bottom: 5px, it actually ends up looking very similar to your first screenshot.