Yeah, I think it's fair to say most people will remember whatever pop songs/source cues are in a film more than the score itself.
In Munroe's defense, TMNT 2007 was a very different beast from the 1990 film, so in a way I'm glad they didn't regress the picture's score for the sake of a musical homage that would go over the heads of most viewers. Badelt's score kicks ass as it is. Plus he was awesome enough to put the full score on his website.
If they really wanted to do a Du Prez reference though the best spot would have been when Mikey is skateboarding down the sewers. Would have been better than the garbage pop song they used in the end.