Why did Honda do it? My guess would be for space reasons more then anything else. Place the shock more upright, and they upper mounts would be higher, thus raising the seat height. I know you actually want the shocks more upright as they work better. (I kind of understand why this is, but I can’t really explain it.)
I know when I first dropped my 700XX of to Ed Teixeira; he actually wanted to change the upper mount for his rear a-arms to make the shocks more upright, better suspension performance was the reason. (He would be the one you want to ask about this.) He ended up not doing it, I think the exhaust was in the way then you would also have to have customers redrill their frame for the new shock mounts, not something everyone would feel comfortable with. (Especially since they new holes would have to be drilled with precision.) I think after he started working with the stock upper mounts, he determined that everything would work out good anyway. Yes, it would be better to have them more upright, but when all is said and done, most people wouldn’t have noticed the difference, especially with a good shock setup.
Next time you talk to Ed, I am sure he can go into more detail. Above is just what I remember in my conversations with him, but that was a while ago. Ed has probably forgotten more about suspension then I will ever know!