Anyone? I'd like to know as well. Bought a 2016 and would like to add a sub. Considering pulling out the 3rd row since I will never use it and having a sub enclosure mounted there. The other option is the storage compartment above the spare tire but I really like having that for groceries, etc. Plus, I don't want to block access to the spare tire, jack, etc.
Remember that the stock audio system sends a low frequency to the subwoofer when the VCM systems is active. Unless you can extract a "Pure" low frequency signal from the audio unit, you may over compensate and hear/feel a rumble. One option is to disable the VCM system. Do a Google search for info.
The 3rd gen MDXes (since 2014) should have identical sub placement. It is the hardest speaker to replace but still not very difficult. You should look under the 3rd generation category and you will find several audio threads there including sub replacement. Personally I recommend replacing all of the speakers - the stock ones are really puny (15W and 20W max, except for sub). Also, be aware that the sub is on a crossover with the rear speakers and not the front so moving the fader forward (cutting rear sound) will also cut the sub.
I have had no problem with the sub putting out noise, so haven't felt the need to disable the active noise reduction system. I am very happy with having replaced all of the speakers - a really noticeable improvement.