Chelsea will have a much more difficult opponent due to the goal conceded in the 94th minute, they did rotate heavily for this game but still - conceding 3 goals against Zenit isn't something they should have allowed. They might regret it really soon.
Well, but by finishing first or second you can basically just avoid difficult opponents in the round of 16. From the quarterfinals onwards, everything is reshuffled again anyway. That's why I don't quite understand the discussion about the group placings. Especially not for top teams like Chelsea. With less good teams it is still understandable, but Chelsea has the claim to win the CL again and then they have to pass against all teams sooner or later.