Football is full of surprises and that is why we see those results playing out the opposite as others thought it will be. You are right, Leverkusen needs to focus more on their domestic league because it will be very hard for them to reach the semifinals in UCL. The reason is that there are so many strong clubs in UCL.
If Leverkusen can improve their performance and take their UCL matches serious, they might go far but they have more hope in Bundesliga than in UCL. However Europa League is not as tough as UCL, so let them know that it will not be an easy win for them in UCL.
What you say is of course reasonable if indeed Leverkusen does not have the depth of a qualified squad later, in my opinion, Leverkusen will try to stay focused on the Champions League and also the Bundesliga next season, as they have done in the Europa League so far, Leverkusen failure in the Europa League is not something that indicates if their squad is weak but in that case of course the mentality possessed by Leverkusen is still far compared to Atlanta, Next season I am quite sure that Leverkusen will be an attraction for good players ,so it is likely that if Leverkusen brings in some new players, then their mentality and also their performance will be strong enough to compete in the Champions League.
I think, Leverkusen will remain focused on the Champions League and the Bundesliga at the same time and I am quite sure if Alonso can optimize their squad to be able to face the tight schedule next season, indeed the Champions League has a different atmosphere from the European League, but when other surprise teams can be quite capable of doing it and going far in the Champions League, Why do you doubt Leverkusen will not be able to do it next season?