Just did my brakes and rotors on my 2010. I noticed one pin is longer than the other. The shorter pin has a rubber boot near the end of the pin. This pin goes on the lower section of the caliper correct? And why would there be two different length pins?

 

I would call that cost cutting, less metal = more profit

On a serious note, I recently did my brakes too and did not notice difference in pin length. While I put brake parts exactly where I remove them from, you should not experience any ill effects if you accidentally swap them.
I believe caliper bracket bores are the same size diameter and length wise.
Whoever did the design of the brakes, thought that it was appropriate for them to be different length, no big deal.