Have both in my crew
I have a 16.5 KTM 450SX-F Factory Edition with the ARO120, my buddy has the 18 YZ450FX with ARO137.
Both are strong runners with exhaust and ECU mapping. The PR2 isn't necessary unless you aren't going to take the time to make engine jackets, radiator covers, and install a thermostat. The engine is better off with all of these things done, once temps are controlled the ECU won't go into flood/choke mode. I had a PR2 on my KTM, it wasn't mapped right and was way to rich, had to send it back. That's a factory edition problem that Jeff hasn't worked out, others with them are super happy and it's a good ECU/Map for most bikes.
The YZ was pretty flat until the FMF full system and power tuner fuel / timing was adjusted. Both also benefited from the drive gears being swapped on the ARO to get the gearing closer to the proper runout for stock counter shaft sprocket. Now it can hang with the KTM for the most part... stock I was crushing it.
I went to a pod on the KTM, the airbox would fill with snow and soak the filter on every deep day. Yamaha is easier, drill 1 inch holes on the intake cover and put frogzskins on them 12-16 holes are perfect, then stuff the intake ports with foam and seal them off.
The YZ has a steeper rake and more over the bars feel than the KTM. The TSS needs to be dropped to the floor on the YZ, also the ball join can be shaved down a bit to get it to squat enough for good steering. (60 degrees of head tube angle is about perfect, we've landed there on 5 bikes now as the sweet spot for climb/turn/ski pressure)
Yamaha wins:
Exhaust is better for engine jacket fitment
Intake is very low cost to mod for snow
also has a kick starter in case of battery failure
motor is bullet proof, most reliable engine ever made
KTM wins:
20 pounds lighter
engine has more bottom end power
gearing is taller and shifting is less on this transmission
narrow and more comfortable cockpit (subjective to preference)
Steel frame has less vibration (snowbikes are often at high RPMs and it wears on you)
Kreft has revalve control that allows you to tune the fork from woods to snowbike valving with a knob (WP only) Air and the Kreft RC makes for a fork that doesn't need to come apart season to season. (Trio would resolve that, but you'll still need tuning on the stock suspension if you're demanding of ideal performance for track or woods)
Take what you will from the pros / cons but it's a matter of your needs... since you are going LT - it would seem weight isn't that important to you. It's why I went KTM... but at the end of the day the yamaha is a more practical snowbike platform.
Hope this helps a bit