For example, https://github.com/Pym/Jasper/blob/gh-pages/_layouts/page.ht... has a <section>. Why not <article>?
Another example, why "page-title" and "page-description" on https://github.com/Pym/Jasper/blob/gh-pages/_includes/header...? Why not just "title" and "description"?
All Jasper's assets came from Casper, so I didn't chose any markup. I just reused Casper templates and translated those for Jekyll :)
Here are the original Casper files related to the two files you mentioned:
[1] https://github.com/TryGhost/Casper/blob/master/page.hbs#L25
[2] https://github.com/TryGhost/Casper/blob/master/index.hbs#L14...
As you can see if you compare both repositories, Jasper is a direct port of Casper but with less code repetitions!
BTW, here is the <article> you're looking for: https://github.com/Pym/Jasper/blob/gh-pages/_layouts/page.ht...
But I can't really answer that second question, I think you'll have to ask Casper authors:
https://github.com/TryGhost/Casper/blob/master/assets/css/sc...