Yes, I read several interviews where John wanted the lower section more out of the way, as the Strat has, for his playing style and large hands, and the reversing the headstock did it. Whatever the reason, he liked the result, which was the point with a signature guitar. It’s his thing. I didn’t like the tuners, for instance, but he did. I can always change them. Like I said, if you’re happy putting a strat-ish neck on it, I think you should do it! That makes it your take on it. Of course, that doesn’t mean anything is wrong with the design as it was. You just like something else, and some might view your “issues” with the headstock as a not so convincing reasoning to change it. Does it matter? Not really. John got what he wanted and you got what you wanted, and everyone should be happy. I hope you are!
The Silver Sky is an undeniable hit of a design for PRS, but nothing’s perfect for everyone.