Several sections, namely GAME, LEAD, RULE, SLOC, WCHR, and WMAP, have their own compare methods. I looked at WMAP in particular, and it seems that the main difference is that it doesn't rely on the getProperty(name) method, which throws an unsupported operation exception for that section. But for many of these it's silly anyway - since that is used to find elements that match, but may have different indices, but yet there's only one of several of these sections - and for others, like SLOC, it could still compare either based on index or tile location.
This would result in more consistency between sections (notably headers, which some of these sections are missing), and reduce the amount of code by several hundred lines.