As stated, the TSB addresses an airflow issue that is essential to prevent overheating of the rotor. It's a heavy vehicle and the rotor/pad size (sweep area) probably should have been sized larger. Heat leads to material surface reactions and eventually non-uniform changes in rotor thickness. That's what creates the sense of pulsation.
To address this:
1) Do the flap modification yourself to increase airflow. It's really a no-brainer. You'll get the best looking (cosmetic) job if you remove and modify, but they can be cut in place with a $5 set of shears.
2) Consider resurfacing and/or replacing the rotors. Once they are damaged, it can be hard to recover them. Cast iron had micropores, and a certain amount of brake pad material transfers into the surface. The action of "bedding the pads" is maybe the single most important part of a brake job to ensure long-term success and good stopping action. If the rotor has been contaminated by silicon carbide or other material, the pad transfer, eventual wear patterns, surface oxidation, coefficient of thermal expansion, etc., will all vary across the surface promoting judder.
3) Toyota recommends resurfacing even brand new rotors, ON THE VEHICLE. Why? because new doesn't always mean perfect. Also, if the hub surface isn't perfectly flat, you will begin life with rotors that move in an oscillating pattern and that will only get worse over time.
4) Do you own a torque wrench? 76 ft-lbs, and in a pattern, going around 2-3x to seat the wheel correctly and uniformly. Your rotor gets sandwiched in-between the hub and the wheel. If not done right (uneven or way over clamping force pressure), you actually bend that rotor at 5 pressure points, which only becomes worse as it heats. If you apply mechanical stress to a metal and then heat cycle it, it takes a new shape! Any time a shop touches my wheels, my Job 1 is to loosen and retorque those wheels ASAP. I use an impact gun with a torque stick around the hub 2x (first to about 10 ft-lbs, then to 50 or so), and then final setting by hand with a torque wrench.
5) Make sure the pins and sliders are all working, and that the pads move freely within the carrier. Drag = HEAT!
6) Driving practice: One thing I try not to do is sit at a light with my foot pressing any harder than absolutely necessary on the pedal. Hard pressing hot surfaces together promotes uneven material transfer.