Test Results:
Singles
Femur Bone: Luck +5
Femur Bone: Resolve +2
Worm: Battle +4
Mouse: Agility +3
Mouse: Resolve +1
Mouse: Resolve +5
Rhinoceros Beetle: Agility +4
Box Turtle: Battle +1
Rhinoceros Beetle: Luck +2
Bundles
Creepy Crawly Basket: Agility +4 and Luck +2 and Perception +2
Bird Basket: Agility +3 and Luck +3
Bird Basket: Agility +5 and Luck +4
Bird Basket: Agility +5 and Luck +3
Bone Bouquet: Battle +2 and Resolve +3
Bone Bouquet: Battle +2 and Resolve +3
Take-Away
So - I don't think there's much of a difference, honestly. The bundles just use the items as if individually. It still awards the same amount of CP per item in the basket.
So I prefer bundles if it's possible. They're used MUCH faster. And, they take less space in the inventory holes if you're stocking up like I was. However when it comes to actual functionality of use, I saw no difference.