Never heard of the shipping pin thing.
I've always aligned the flippers to the biff bars/dots, which correspond to the flier picture. Seems weird to me that Bally would "incorrectly" align all of their flippers just prior to taking their playfield reference shots for every flier they released. If they're supposed to be aligned with the ball guides, why wouldn't they have done that before taking their product pics of the playfield?
Frontier for example plays like crap when you align the flippers to the ball guides. Much less power to the spinner/inlines. Same is true with Flash Gordon. Aligning the flippers with the ball guides will make it easier to trap and put more power to shots at the center of the pf and less to the shots at the outside.
If you want a lot more gas shooting the bear target/pop bumpers, by all means - align them to the ball guides. I'd rather have more power in the outside/spinner shots.