It's simple enough and although I think making it simpler by making it a straight whoever finished higher, I don't mind that. It gives some merit to knocking out the better teams that might finish higher and passing on some of that merit to the later knockout rounds.
The idea of seeding is to increase the likelihood of the two best teams being in the final, the 4 best in the semis etc, this could make that more likely, especially in instance like last season where PSG were obviously a better team than Arsenal later on in the season despite them finishing 15th earlier on.