The more semantic you make your HTML, the less that this tends to matter. Right now I'm actually <section>ing and <article>ing my way around my site, so when I want to change the design, I head straight for the one place it's actually described: the CSS.
Not to mention the template mechanism. With my (home made) site generation tool, I changed the whole design of my site by changing exactly 2 files : the template, and the css.
I'm not exactly sure what you mean, but if you run jekyll --server --auto while in development any small change you make gets automatically regenerated and it only regenerates affected files.
I didn't know jekyll had a server. If it does than it's not exactly static blogging anymore.
It is a server for testing purposes, like seeing how you site will look before uploading to your webserver