Hi Alistair,
I found a bug that was stopping the highlighter notes showing correctly and will have a fix in place in beta 11.
The scaling should stretch the highlighter notes to the height and width of the song display automatically (stretching as you described). The song autoscale logic is way better in v6 and scales properly rather than trying to adjust font sizes as in v5.6. I am hopeful that most highlighter notes should match reasonably well, but if not, it will be the scaling logic between v5.6 and v6 that causes discrepancies, particularly songs that displayed as multiple columns (where v5 didn't do this very well).
The highlighter effectively takes a screenshot of the song display (full autoscale or width only autoscale) to place below the highlighter edit page and creates a png file that matches this window size. It shrinks the song so it fits on the edit page for highlighting. When the highlighter is displayed, the highlighter file is then stretched to match the scaling of the song (width and height).
Can you let me know how beta 11 displays the notes and how far out they are before I look into the idea of margins, etc.
Unfortunately due to different devices and resolutions, synchronising highlighter notes will never be perfect.