I think your concerns are little misguided:
First of all as you have mentioned it already patents are to protect one's intellectual property. I'm sure you are aware that Toyota didn't invent car, Atkinson cycle engine, NIMH batteries, electric driven cars (those were actually in use at the beginning of 20th century) etc. etc. etc. I'm also sure you are aware of the fact that Ford and Nissan use Toyota hybrid systems in some of their cars, so Toyota had to provide them with detailed technical specs to match rest of the car, even if the hybrid parts are shipped fully assembled from Toyota. That's how our whole education system works, in mathematics, physics, engineering, you take best work and their ideas, analyze it and then improve on it, otherwise we would be still living in caves , reinventing wheel over and over again. The fact Toyota is a leader in hybrid technology, makes it a natural target for this type of deep engineering analysis. This is how it's done, everywhere , from AMD analyzing Intel CPU and coming out with competitive design, at some point being better than original, to Japanese car makers looking at our SUV, mini van or pickups and improving on them. Does it bother you it's published on website so everybody can read it? Because people who actually can use all that info, will have it no matter what, I'm sure GM, Ford and other large companies did their own strip down analysis, probably much more detailed, you just can't access it. The whole report does not have any info, that anybody with proper tools and schooling couldn't get on their own.
I think it is very flattering they actually spend all that money and time to analyze and study this design , it shows how far ahead of everybody else Toyota is at the moment. I heard somewhere it used to be Japanese that would come here to look, study and admire US factories years ago to learn newest technologies, now we dissect their cars to learn.