Although Atalanta sometimes managed to make a surprise in the Europa League and in Serie A but still, to make a surprise in the Champions League is not easy at all. So yes, even though it currently has a new format but I'm still not sure Atalanta is able to advance further in the Champions League. but even so, at least to qualify for the last 16 or maybe the quarter-finals basically Atalanta still has a chance but of course it won't be easy.
Surprise has different levels and years ago, Atalanta already made big surprise in Champions League. That year, in 2020, they went to Champions League quarter final and I am sure with you, their quality and position in 2024 season is better than years ago. They just won a first title in Europe, Europa League title last season. It increases quality and confidence of Atalanta a lot and they can go through group phase in Champions League 2024 - 2025 season, they can do it.
I am very sure Atalanta will make it to the round of 16 in the Champions League. Despite that, I believe they will qualify for the round of 16.
I do not know if they will make it past the round of 16 because I don't know who they will be paired against, but I know they will get to the round of 16.
Going through group phase is possible and achievable for Atalanta but farther than that, I am unsure. It depends on their next opponent after group phase and always enough of luck. Knock out matches in Champions League can be decided by one or two single moments and if Atalanta play well, have enough luck they can go far.