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The smallest minimum dimension is the brisket hence it will cook faster. Since verticals when low and slow are hotter at the top the butt goes there.
I like SmokinEdge's flavor argument. Nice it agrees with the science
I always rotate from top to bottom, and back to front once or twice if it is a wood burner no matter if it is all pork.
A good question though when mixing pork and beef. I ran ribs and a chuck roast a few weeks back but never really thought about what was on top.