A comment on your site: I have to zoom to 300% on firefox to get what seems like a 'natural' view. Without this it feels like I'm viewing a pdf. This is not serious criticism, but something that bothered me a bit. Others may feel differently.
As for the pdf look, you're right. The problem I encountered way back when I was actually building the site was that I didn't know what to put on the extra margins. I could've put footnotes and figures, but that's pretty hard to do if you're generating the site from markdown without a custom markdown engine. I'll see what I can do about it tho, and if you have any suggestions for how I could improve this I'm all ears.
In any case, keep on writing!