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.