Rampage, the "reasoning" for this 2016 rule change was the following:

Effect: Eliminates multiple spots of enforcement for a double foul after a change of possession.
Reason: Simplifies penalty enforcement.​

Ostensibly, the rule change was put into place to make things simpler.

My take: the NFL has clearly stated their intention to give teams the incentive to accept touchbacks and start at the 25. The kickoff return is considered to be the most violent play in the game, with large men running at each other at full speed. The chance for life-threatening injuries are highest during kickoff returns. The NFL is (supposedly) interested in player safety, and they do not want the bad publicity of a major injury happening during a kick return.

THEREFORE-- the NFL passed this rule knowing that it had the potential to disproportionately punish the receiving team. The NFL adjusted the rules to make it even more clear that returning a kickoff is a big risk for field position.

I think there are many ways this new rule could be tweaked so that it does not punish the receiving team so disproportionately. It will be interesting to see how other fans and teams react when this rule is applied in the future.