I don't disagree. It plays huge part in the problem. Watching that game countless time, I think another part of the problem is still the way SAF approach game (the first leg is a vital one that decided the tie than second leg). We played Carrick Fletcher & Scholes in midfield, but differently than later years. Scholes played more purely as no 10. Carrick & Fletch were utilized more of box to box role which never suits Carrick & it let too much space for Kaka in his prime to operate just before our (make shift) defense line. In later years, it would be Carrick sits deep, the 2 other midfielders or a roaming forward play hybrid roles, no traditional no 10. That's truly more 3 men midfield. What SAF did were trying to blow Milan apart meaning we're also more open to be countered. That midfield is more like what Mourinho is trying to implement with Herrera being Carrick's (misused) position, Pogba in Fletcher place & Mkhi or a new no 10/ second forward next season in Scholes' place.
SAF in latter years approached game better. We lost Vida & Brown vs Barcelona next season & we still pretty approached the game the right way. The blend between being defensive & attacking was better, not just on personnel level but also tactical level. Less space between the defense line & midfield like with this AC Milan game even for home game where we go for goal on other end.
Edit: (bolded part) Rewatch Kaka's first goal. Neither players positioning wrongly Heinze & Carrick. Just that the tactic, roles assigned to them asking a lot for them to step up taking responsibility (CB step into midfield, a part of 2 men midfield has to drop deep pick up floating attacker playing in pocket of space) which against their natural game: Carrick doesn't like to running around alot; Heinze doesn't like to a foot race with attack which he's either close to them when playing on the wing or trying keep distance so he can recover with last ditch tackle. Kaka was just tactically deployed perfectly to destroy both of them