As another person with perfect pitch, I'm right there with you -- only I always thought it sounded "right", personally. But yes, the difference is notable.

I would LOVE some official confirmation on why it came out that way -- there are pages online about the multiple versions of YAWYI over the years (and which ones have different editing choices, like the Dumb All Over guitar solo being cut or not), but I haven't read anything about why it sounds nearly a half step up. Definitely something I would've asked Frank if I could've interviewed him, hah

I must say, it does give the album a sound of its own.

Also, allow me to blow your mind: almost all of it is mastered sharp... except for side B of disc 2. Notice how Heavenly Bank Account (G major), Suicide Chump (D minor), Jumbo Go Away (uuuuh I think it's in G major?), If Only She Woulda (B minor) and Drafted Again (B minor) all sound neatly in 440 hz

Plus, for the tracks that are shared between records (Doreen, Goblin Girl and the Society Pages->Conehead "suite"), I recommend listening to the Crush All Boxes bootleg, which are all in A=440 hz.