Its politics, the reality is that dealerships are more of a franchise than a direct arm of Toyota; they are all owned and operated by private companies/persons under a Toyota license and are in their own right to manage their business however they feel they should. Toyota does have guidelines and expectations on how its dealerships should operate and what SSTs they should be using, but there isn't a lot of enforcement on that from the corporate level from what I have seen in my personal experience/opinion. I've talked to a few factory guys and they basically lament over the same thing as well, the reality is that the same style of penny pinchers that run the dealerships also tend to run larger corporations such as Toyota. So the idea of creating a costly and time consuming "task force" to enforce their guidelines is something most bean counters will think is useless while the field/technical guys absolutely understand the need for it.
In this respect Toyota in my opinion isn't any different than other brands, I hear horror stories of a lot of dealerships regardless of the brands. Just the internal conflict between Lexus and Toyota seems ridiculous to me, let alone the way the Lexus dealer tends to treat Toyota customers seeking service (though some of that has to do with the way Lexus/Toyota is structured if I remember right.)