I think they just realized that people will actually pay more for the 3.6, and decided that it was more beneficial to add eTorque to something that has a higher sales cost.See, that was precisely FCA's issue with eTorque: it assumed that it could turn a regulatory issue into a profit opportunity by simply adding eTorque to the options list. But the vast majority of consumers failed to see the benefit for them, and the motor flopped.
Again, Ford showed how it is done with EcoBoost.
There's a reason FCA chose to remove eTorque from the Sport & Rubicon first... my guess is that the Sahara sells the most volume and will therefore have a greater impact on CAFE. Profit percentage on a Sahara may be higher than other trim levels as well. Obviously this is all speculation, but after viewing the annual eTorque shuffle this looks to just be about finding the right balance between production cost, sell price, and CAFE fines.