Flick wasn't assistant last season, and Bayern played defensive in both games. Flick has fundamentally changed the way Bayern play, they play a much higher line, press aggressively from the front and move the ball much quicker and use the width of the pitch to a greater extent. Kimmich was at Right back which is now Pavard, Alaba was at Left Back which is now Davies, Muller & Goretzka were on the bench, Neuer was still recovering from his injury, so they have changed quite a bit since they met Liverpool.
There wasn't much wrong with Bayern back in 2018 when they lost the semi vs Real, they were the better side in both games and should have faced Liverpool in the Final which they probably would have won, the 2018/19 season with Kovac was an example of an incompetent manager making a mess of a fine team, Bayern realised early enough to rectify it and went back to the level they were before, this time with Flick instead of Heynckes. So the games with Liverpool are not an accurate reflection of the this current Bayern team.