The fact that Bayern Leverkusen were undefeated until the final of the competition shows that they are very strong. However, a team that competes for a full season and is still beaten till the final is not a weak team, and that doesn’t mean they won’t perform as we are saying in the champions league.
I believe they can do it even in the champions league competition, even if they will perform the same as they are doing in the Bundesliga, because I know the Champions League has many more strong teams than the Bundesliga that Leverkusen have already used to, so the thing here is that Leverkusen will not be beaten in the champions league, but with their current status of performance, I believe even if they don't top the table, they will nearly make it to the top.
You are right, Leverkusen's loss at the end of the season doesn't mean that they are a weak team. Leverkusen has the strength to maintain their unbeaten streak next season. However, Leverkusen were unbeaten in the Bundesliga and did not lose any of their Europa League games till they lost the final to Atalanta. Leverkusen performed well throughout the season, even when they lost to Atalanta in the Europa League final, I wasn't surprised by the loss because they had performed at a high level this past season, and they are human, they will be weak in some matches, we shouldn't expect them to have the same record in every game they play.
I am confident that Leverkusen will have no challenge in their next Champions League games, we have seen how they dominated the Europa League this season, despite losing at the end of it. Xabi Alonso is a manager with Champions League experience, and I believe he has strategies to prepare for managing his club in this competition.