I have discovered the bar across the back window is actually very well thought out by Toyota. It is the perfect hight to block the headlights of all the people tailgating me as I cruise around 5-10 mph below the speed limit.
Actually I find it is also at the "right" height to block the glare from the headlights of cars behind you from hitting the sensor in the rear view mirror on Advanced models, meaning the mirror will NOT DIM the reflections of the lights from the vehicle following you. Since there is no way to manually dim the sensor equipped mirrors this creates a potential safety defect since the glare from improperly set headlights can potentially blind older drivers because the time it takes for an older person to recover from excessive glare takes a lot longer than it does for a younger driver. Additionally since the design of the light sensor uses a cheaper type of photocell than the type used in European cars, the sensor DOES NOT respond to the spectrum of light from HID light sources and provides no relief from the excessive glare from all the drivers out there who are illegally using HID lighting kits in headlight fixtures designed for Halogen lighting sources. It goes without saying that there is no legal way under USA DOT rules or any European lighting standard to add HID lighting to a light fixture originally designed for Halogen lighting. NONE of the kits sold will legally claim they are street legal in the USA or meet DOT FMVSS-108 requirements. Because of this I have formally requested a safety defect docket be opened with the NHTSA to see if enough complaints are logged to justify opening a formal safety defect investigation.
Sorry to hear that you are having this problem. I have the auto dimming mirror in my base model, and it works fine. I tested it by turning it off with lights shining into the car from behind, then switching it back on and watching it dim. The one I have is a Gentex by Mito Corp. I had the dealer add them to my '04 and PiP, and I believe it is the same kind as came in my '06 from the factory. Tailgating a Prius seems to be a popular driving style here in So Calif but lights haven't been a problem for me. With a little help from my son I figured out that if I can see the license plate of a vehicle through the lower portion of the rear hatch, that vehicle is too darn close.
My mirror works well except for if a truck is 50 - 75 feet behind me. That's the dead zone where the lights get reflected into my eyes, but the black bar casts a shadow on the sensor, rendering the auto dimming useless.