Nice changes! I like the Chapter segmentation for highlights and the selection handles are sufficiently non-offensive to me now!
A few notes of feedback/suggestions:
1. Only top-level chapters/sections show up in the highlights panel - it would be nice for it to also segment them by sub chapters as well. Here's a screenshot of one book - the four Parts consist of dozens of shorter chapters, which aren't showing up.
2. It seems strange that there is both the Edit button and the clickable Edit Notes link. I see that they do different things, and actually like the larger notes-only editor, but the two buttons so close to each other is uncomfortable in some way...
3. If there could be just slightly more space between highlights in the highlights pane - a pixel or two - that would be nice. I know that each line is a new highlight, but they tend to blur together.
Nice work! Any estimate on when Calibre 5 will be released?