An object itself does not have bounds. And if I attach a DirLight component to an object, what would be the AABB of the object? Or if I attach multiple components to the same object, eg. a RenderableMesh and a Collider. The Collider can be "bigger" than the actual mesh which means the two component's bounds are different. This was the reason why I decided to store the components and not the objects.
Since QuadTrees are used for collision detection (object-object, object-line, object-frustum, etc), the collision bounds should be used for placing the object in the tree. That means Collider component will give the position and size of the object that is used to place the object in the QuadTree.
Or do you want to use the tree for a different purpose?