I agree with you. UCL and UEL are on different levels. Atalanta were impressive in the Europa League and even managed to beat Liverpool who often play in the Champions League. But now Atalanta are really playing in the UCL. I am not sure Atalanta will be able to do the same as they did last season. All the top European clubs are in this competition. They will always be motivated to win the Champions League.
I also don't think Atalanta can beat Liverpool in Champions League this season if they meet again here and I have checked all the matches here but I didn't find any matches for both of these teams or did I miss it maybe because this season the format is different. But what you said is also quite logical that it is still not certain for Atalanta to repeat the victory if the team is faced with an opponent like Liverpool again in the current condition. Because Liverpool also have not been worse with their new coach this season and it has been proven in the early matches this season in the domestic league.
Atalanta qualified for the Champions League after they won the Europa League trophy last season, Atlanta journey in the Europa League last season did surprise us by beating two favourites teams such as Liverpool and Leverkusen, but still last season and this season we will see a lot of differences and also changes that has occurred from the squad, performance and consistency of all the teams which play in the Champions League, so I think the chances of Atlanta beating Liverpool if they meet again are of course very small, besides that Atalanta not an experienced team in the Champions League so far, so it is difficult for we to say if they can be make surprise us again like they did in the European League last season.
Atalanta in my opinion is quite lucky so far in the Champions League draw because they avoided the big teams in the league phase, because of the 8 matches they played, only Arsenal make the potential team to trouble them later, while Liverpool is actually a very difficult after they are meet with teams such as Leipzig, Madrid, Milan and also Leverkusen, so I think Atalanta chances of qualifying are obviously greater if we compare than Liverpool currently have.