There are various reasons for why instruments are tuned to different notes. Mostly it's due to the timbre (sound color). The clarinet has always been in Bb AFAIK.
Even with a Bachelor of Music Performance in my collection of degrees I've never been able to wrap my head around instrument transposition that well. It's probably because I'm a guitar player, where what you play is what you get (or at least what you wish you get).
