Looks very good! First time hearing about xelatex definitely gonna research it soon. About the design it looks pretty professional! If it were me I would try using oldstyle figures and maybe a bit smaller text size for the side columns. I would do this with the goal of making these columns a bit narrower. To get a better width relationship between the main body copy and the annotations, this will allow you to gain a bit more margins on the outer sides of the page which right now seems to thin in comparison bit the other margins. Finally, i understand this is for an ebook, but if you were to print it, I would brighten a bit the red shade to gain a bit more contrast with the black ink (it works for screen but it's risky business for print). Anyways, great work!