Atleti was hit by the transfer ban at the time so they couldn't strengthen their squad. Also they were surprisingly bad at the group stage last season. Couldn't even beat Qarabag in two matches, not even scoring one goal! If Chelsea and Atleti meet again I don't think Chelsea can beat them.
Of course Chelsea could beat Atletico. Much fairer fight than Barca vs Roma, but unexpected things happen in football even on 2 legged ties.
I do expect Atletico to be better than Chelsea next year, maybe a sizable difference, but their talent is close enough overall that on a good day Chelsea can beat them.
I do think Chelsea is going to take some time to gel. I think losing CT will cost them and there is no way Kepa won't be a drop off in organization/leadership if not shot stopping and positioning drop off as well, because CT was just that good and settled there. Then you have language adjustment, cultural adjustment, not knowing the EPL players. Then you factor in new coaches, other superstar players maybe wanting moves that won't get them--it will be hard to get that train in one direction.
But on any given day Chelsea is still a dangerous animal.