I think Father Figure just didn't fit on that record period. It's obviously something Rich wrote before AOA were formed, it sounds sooo Filter, not a bad song, just out of place on that record, it would have been better on 'The Amalgamut'.
As for Rich and his father, they are actually really close, maybe they weren't at one time though. If you watch the making of the 'Take A Picture' video (I think it's on Youtube), Rich's dad is on the set and Rich explains the lyric 'Hey Dad what do you think about your son now?', the song was written about a time Rich (during his alcoholic days) got wasted on a plane and took all his clothes off, hence 'what do you think about your son now?'. I love that lyric and that song though because it can be interpreted in many different ways and that part in particular is just so powerful.