Actually the HTML is minified as much as it can be (or close enough anyway). The problem is, with HTML you can't remove space between tags entirely as it changes the behaviour of the HTML.
Simple example: <b>Hello</b> <i>World</i>
You can't remove the space between those tags because your text will say "HelloWorld" instead of "Hello World".
The best you can do is collapse all space down to one whitespace character, which is exactly what we do (using newline instead of space). If you look at how other systems work you should find they do the same - I know CloudFlare does.
Incidentally, Q2A's minification also has an extra speed benefit because it actually reduces the processing time on the server. In other words, the actual PHP code in qa-theme-base.php is notably faster if indentation is omitted.