I'm sorry but I think people are concentrating on the wrong aspect of the law here. For me, the primary question is not whether the player challenged for the ball and/or what exactly 'challenging for the ball' means.
As far as I'm aware, the additional, recently-added wording was merely a clarification to, and was even supposed to be a strengthening of, the existing prohibition on an opponent even being in the penalty area in the first place when the free kick is taken. That is still the primary consideration - it's still in the law, it comes first in the law and is still fully applicable.
Even within the section of the law quoted above, the 'allowability' of a player being in the area and then challenging for the ball is predicated on the opponent not having enough time to leave the area before the kick is taken. Looking at the full incident, starting from when the IFK was given, I would say the Beşiktaş player had easily enough time to leave the area but chose not to.
Although not saying so explicitly, it almost seems as if some are looking at this as if the law now means it's OK for the opponent to be in the penalty area when the kick is taken, just so long as he doesn't go on to challenge an opponent (or touch the ball) - it isn't.
The opponent is still not allowed to be in the penalty area before the ball is in play and the additional wording, which was brought in (as far as I can tell) mainly to clarify the scenario where a player cuts across the edge of the penalty area to close down an opponent, does not alter that.
So for me, this should have been a retake, not because the player challenged an opponent but because he was in the penalty area, had enough time to leave and did not do so. While being in the penalty area is often overlooked because it doesn't have any effect on play, it is still against the letter of the law and especially when it then contributes to a situation which benefits the team of the player having breached the law, I think there's a good argument that it's against the spirit of the law as well.