Even though Atletico Madrid are currently in fifth place, I have no hesitation in saying that they will still finish in the top four at the end of the season. Indeed, currently Atlitco Madrid's performance in Laliga is not as good as in the UCL league, they even managed to get rid of last season's UCL league runner up, namely Inter Milan, and now in the top quarter they will face Dortmund, of course this is their main focus at the moment.
Their chances of getting into the top four are still very wide open because they currently have no more matches against teams like Real Madrid and Barcelona on the sidelines. They will even face Bilbao at home and this is one of their opportunities to overtake Bilboa in fourth place with a difference of only one point. So I believe Atletico Madrid will still fight in the league to stay in the top four, their current performance cannot be said to be bad after what has happened in the UCL league.
It seems to me on the contrary, Atlético’s chances of reaching the top 4 are falling due to the fact that they have a good position in the Champions League. If they can beat Dortmund, then on the way to the final one of the pair PSG - Barcelona will be waiting for them (this is much better than Real, Bayern, City or Arsenal as in the second branch to the final). Maybe it will turn out that they will give all their strength (due to motivation) in the Champions League and lose points in La Liga. I wouldn’t be surprised if they lose the head-to-head match to Athletic and worsen their situation.