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.
You're right. UCL is higher level, UCL has more stronger teams. Winning UEL doesn't increase the chance for the success on UCL.
Well, it was quite surprising that Atalanta could beat Liverpool in UEL. But now in UCL, I'm not sure that Atalanta will have a chance to beat Liverpool anymore. We can see that the performance of Liverpool looks more stable and convincingly. It is quite different with Atalanta which looks very inconsistently in domestic league. They got 2 losses in 3 early matches in Serie A. This can be a sign that Atalanta is actually weaker than the previous season.
It can even be said that the current Liverpool squad is reliable enough to beat Milan and it is certain that Milan will not be able to do much later. We know that in the domestic league, Milan is so down and it is very difficult to get positive results and on the other hand Liverpool can always show something different.
If we consider their current performance in domestic competition, Liverpool looks to have a better chance to win. AC Milan performed badly in Serie A, maybe caused by a new coach and many new players as well. But when it is in UCL, sometimes a team can perform differently. However, I still favor Liverpool to win the match although it will be in AC Milan home. I assume the current game play of Liverpool looks move convincing to win any match, including in UCL match.