Atalanta coach is an experienced coach and he was able to understand Leverkusen game tactics which gave him an upper hand in that match. Since he understood their game tactics, he came up with a game tactics that will outsmart that of Xabi Alonso which he succeeded, and that was why you see that Leverkusen was unable to face and calm down the pressure on them after the first goal.
Xabi gat no other option or tactics to use and he saw it that Atalanta coach has used experience over him which was what made all his effort in vain. From history, Leverkusen is always finding it difficult to win Atalanta and that was what still played out that day, and this is why I will agree with you that Leverkusen never underestimated Atalanta. It is same with Liverpool.
Gasperini has been building Atalanta since 2016, he certainly understands the strengths and weaknesses of his team more than anyone else, it is very natural why his tactical quality is able to beat Xabi fleet which is at the peak of its performance. Indeed, there were lots of wild issues that developed after the Europa League final, but I think it was a pure victory. However, Leverkusen should be appreciated, they have kept us all entertained with various surprises this season.
If we look back a little, the habit of Serie A representatives tends to play defensively, in this case Atalanta also implemented this strategy. Leverkusen played too openly and focused on attacking, so that when they lost the ball, it was quite easy for Atalanta to carry out a deadly counterattack. Dominating ball possession is not always effective when dealing with a team that tends to defend. Armed with his long experience with Atalanta, Gasperini managed to end the season with the Europa League trophy and a ticket to the Champions League.