No, it currently only works for PrimeTime shows on ABC, CBS, FOX and NBC. It's extremely unlikely it'll be extended to other networks (mainly, due to a lack of correlation between hard drive space and viewership).
Seek help :). With Auto Hop, you have two options -- before you playback a show, choose "no" from the Auto Hop pop-up or keep Auto Hop on and hit rewind after it skips the commercial block.