Yeah I got the impression that the stages may have touched at separation too. Similar to the situation they had with one of the Falcon 1 test flights. Mind you we have to remember that stage 2 was inert so presumably the live stage 2 will have ullage rockets which will aid with stage separation. Maybe a couple of extra retro rockets on stage 1 would help with separation distance. IIRC they had the opposite situation during the Saturn V development when they reduced the number of retro rockets on the S-1C from eight to four which directly translated into extra payload capacity which was utilised during the last three 'J' series missions.