1. Actually, there were quite a few changes in the group when the OFLC was disbanded and its actions and responsibilities split up into the Classification Board, Classification Review Board and Attorney General's Department. For one, all the rules related to the guidelines and classification meanings went to the Attorney General's Department. If you want to blame anyone, blame the AGD.
2. That's what they do. They can't inform you to choose something which another entity has declared illegal for you to bring into Australia.
3. It's not the same game. There's new content, part of which is, according to Sega's website, "2 brand new exclusive levels unveiling an insane side story featuring two angry and armed strippers!" There is a high possibility the stripper scenes might be the meaning for the new rating.
Edit: there's also new weapons and a new "baby mutant threat." These are further things, in addition to Choc's visuals idea, that could very well justify the difference in rating between the two games.