The problem with the current 3 man midfield and no wingers to track back is actually De Jong's role.
I know De Jong has been performing very well this season, and even if he isn't very creative for a distributor his long balls have actually been accurate, but that's not the problem.
The anchor's role requires intelligence more than anything else. De Jong plays very differently to Van Bommel or even Montolivo when he was used there last season. De Jong's movement is more vertical, in attack and defense. When in possession, he drops back to receive the ball and distribute it, and when out of possession, he usually drops until the edge of the penalty area to bloack that zone, with Zapata following the prima punta around and Mexes/Bonera covering.
Compare that to Van Bommel, who's movement was more horizontal; screening the width of his line hence allowing the side midfielders to stretch further and hence close the wings. Montolivo was doing the same last season, and with El Shaarawy tracking back the team actually had a 4-4-1-1 shape in defending with the right central midfielder (usually Flamini from January onwards) shifting to the right flank. When Niang played, it was a 4-5-1 in defense.
At times this season Allegri used a 4-4-1-1 with Poli and Muntari on each wing. This harmed the team offensively (for example there was absolutely no reason to use it against a Chievo side that was lying in the bottom of the table), but defensively it left no space to be exploited. Barcelona, Chievo, and Ajax hardly had a sniff when Milan was compact.
The point is, Muntari is a good ball winner, but Montolivo/Poli aren't. Neither is Nocerino when he fills in for Muntari. With the Christmas Tree formation, the shape is very narrow in defending and hence the fullbacks are left exposed against the opponent's wide attackers.
Against Roma, Gervinho ran riot behind De Sciglio because De Sciglio had to cover an entire flank on his own, and go forward as well because a big part of Milan's attacking strategy was crosses from De Scigilo and Emanuelson. The same thing happened in the derby. When Inter started to bombard us with one attack after another, Nagatomo was probably their most dangerous player due to exploiting all the space on his flank. It was Jonathan's cross to Palacio that almost won Inter a penalty, and the goal actually came from a Guarin cross on the right.
The Christmas Tree formation allows the team to press very high up, but the team can't keep up the pressing for 90 minutes and thus suffers when the pressing stops. The Ajax game at San Siro is a good example of the Christmas Tree vs a 4-4-1-1 (in the case it was a 4-4-1 as we were a man down). Pre-Montolivo's red card, the team was pressing Ajax in their own half (just like the first half in the derby), and in fact Montolivo's red card was due to this. After the red card, when Mario dropped as a right midfielder and Muntari went to the left, Ajax had all the possession in the world but couldn't create a single chance.
Milan's performance against Inter was similar to Ajax's - naive. Had all the possession, but couldn't do anything useful with it.