It's not the 3rd level headline which is the same size as the body text, but the *4th* level headline.
That's in line with what every single browser default style does and what is recommended by the W3C. On the other hand the lower you go with your levels, the more likely it is that you're doing something wrong with your page structure (depending on the kind of document, but in most cases that's true).
I personally would have preferred to give all headings a different font and colour, that would distinguish them from the rest. But we decided against that. The font is the same as the body font to make it as compatible with all different languages as possible. Not sure why we didn't go for a different colour (a bit lighter), that probably was more an artistic decision.
We decided to remove the section indenting because with the now fixed width of the template it takes away too much space and doesn't look good. It's still in the "content.css" file but commented out. So, you can simply remove the comments around it and you'll have it back.