Sure, Atalanta isn't as strong as Liverpool. But Atalanta is possible to beat Real Madrid. Atalanta have defeated some big teams this season, they could defeat a team like Napoli, Roma, and AC Milan. Even if Atalanta defeated those strong teams in domestic competitions, it can reflect the strength of Atalanta this season. However, Atalanta isn't a team that has a very good record playing at their home. So, it makes sense if you assume Real Madrid still can beat them and get 3 points. Moreover if Real Madrid played with their best players. Real Madrid squad quality looks a much better than Atalanta squad quality.
People who said Real Madrid is better than Atalanta because Real Madrid have a good history in Champions League and domestic league, they have more money, they have star players and their popularity is really huge.
This completely different to Atalanta who don't have any good history in international league and domestic league, not a rich team, less star players and they're not popular.
But, if we judge from the current performance, Atalanta is better than Real Madrid.
If Atalanta is 95 from 100, Real Madrid is still 80 from 100.
I agree with everything that you said, Madrid has all the superstars in the world from the history and is the strongest in European competition. However, Atalanta only has average players that looks very strong due to their current form. When analyzing on a football match, you check if the teams are in form or not. Real Madrid is not in form like previous seasons which gives Atalanta the chance to win the match, because they are in form.