Yes you are right Atalanta has almost certainly made it into Champions League next season since they are six points ahead of Roma with only few games left. Beating Lecce recently made it even more likely they will get in which is great for team. However I do not think they played well in that game and if they want to do well in Champions League they need to get better players and play better overall. Just getting into competition is not enough they need to be able to compete with best teams in Europe and right now it is not clear they can do that.
It is almost impossible to catch Atalanta's points. Even if they lose to Torino and Fiorentina in the remaining matches, it is impossible for AS Roma to overtake Atalanta because even though they are both on 66 points, Atalanta is superior on goal difference.
And talking about the opportunity to qualify for the Champions League, I think if Atalanta can win the European league, they will definitely qualify for the Champions League group stage next season. If Atalanta were in a situation where they finished outside the top 5 but managed to win the European league, would Italy have 6 representatives in the Champions League? I'm a little confused by this rule.