The main difference, only difference I believe, is that home runs are regressed to an expected number based on league average flyball to home runs %.
I've heard some people don't like using statistical regression like that since you can make the argument that some pitchers give up hard hit balls so they would have a higher flyball to HR ratio. Same with ground balls. Maybe a sinkerballer has a higher GB% rate, but they may also be giving up harder hit ground balls resulting in more hits.