Here is a site that I customized for HTML5 output:
http://help.zebrazapps.com/I set a bunch of style settings in the skin editor, but then to move the search box and modify the corners and add some extra text, I ended up modifying the default.htm file in the output. I was able to modify the necessary styles and objects in the default.htm file, so that was the only one I had to replace after each build. In fact, I stored the modified file in a separate directory (so it wouldn't get written over), then I created a bat script (Pretty easy, something you can do in Notepad) to copy the modified file to the output directory. Then I'd run a build and double click the bat file on my desktop and you have that particular output.
The style was created by the client; one of their main requirements was that it look decent on a small screen, but they didn't want to use the mobile skin.
If you look at the source of the default.htm page you can see all the edits I made post processing. (I also stripped a bunch of code out of this file that isn't needed if you aren't using a left-side menu.)
*Edited 4/3/13 to fix minor error in last paragraph ("right-side" changed to "left-side").