I agree with you that Hansi Flick should rotate players in a safe match like this so that the main players can maintain their fitness, especially with the increasingly tight competition in La Liga and the big challenge in the Champions League that awaits. Giving opportunities to young players or reserves can also be a good step to maintain squad depth so that the team's balance is maintained.
Rotation might be possible in cup games, or even against Atalanta today, although Flick might want to keep his place in the table to gain an advantage against his next opponent in the knockout stages. In La Liga, Barcelona don't have the luxury of rotating their young players because they need to think about how to get back into contention against Real, who have already extended their lead considerably.
I think they will not use rotation players in this match. Barcelona will want to use their best squad in the Atalanta match. Because a win will be an important win for Barcelona. Because they are in a much more ambitious position in the Champions League. Of course, they will want to hold the reins in the Spanish League, but the Champions League is more important right now. They have many matches to play in the Spanish League, but they play fewer matches in the Champions League and stand out more. That's why I think they give more importance to the Champions League.