I have a Prodigy P2 installed in my 2012 4Runner - which I suspect has the same or similar dashboard and console as your 2016 - and love it. For the mounting location, I ended up going back and forth - in the cubby hole, hung on the dashboard (avoiding the knee airbag), in the glovebox somehow, etc, and ended up making a mount that just slips into the cup holder. The controller lifts out in about 2 seconds and hides in the console when parked at trailheads and in dark alleys - no point in arousing curiosity about the interesting-looking techno-gadget amongst the after-hours "shoppers" - and it's easy to access the manual trailer brake lever if needed.
It was a bit of a chore cutting the hole for the wiring in the front wall of the cubby hole; just be careful with the Dremmel tool and Exacto-knife. I actually ended up taking the center stack apart enough to get the cubby unit out and sitting on the workbench where it was a lot easier to work on. The only thing forward of the front of the cubby was a section of heater/defroster duct - no wires or anything too fragile. Not a lot of clearance, but plenty of room for the wiring to pass through, then under the dash and over to the vehicle factory brake wiring behind the driver's side kick panel.
Note that apparently it's advisable to add an extra ground between the factory trailer wiring plug and the controller. In fact, the adapter harness from e-trailer comes with the extra ground wire already attached:
Tekonsha Plug-In Wiring Adapter for Electric Brake Controllers - Toyota and Lexus Tekonsha Accessories and Parts 3040-P and they say that without a good ground the controller may not work consistently. I'm guessing that the same harness would work for both 2012 and 2016 4Runners.
As an added benefit, if the passenger notices that the driver has dozed off, the brake controller can be grabbed and briskly shaken, causing the driver to be jolted back the task of driving. I'm only joking about this - please don't do it and then sue me.
Finally, three words of advice: Transmission Oil Cooler. Not joking about this.