Tyler I contacted  Rogue about this and this is what I got back.
There are certain items on the 3 ship free list.
When purchasing 3 items from this list they ship free. If there are other item on your order not on the 3 ship free list you are charged shipping for the other item(s).

The bundles are on the 3 ship free list, however, the bundle is considered 1 item (not 3 separate items) so 3 bundles would need to be ordered to qualify for the 3 ship free.
Yes, there are 3 ship free items that make up the bundle, however, the bundle is considered a separate item.

Rogue set up the bundles.
There is no way for Rogue to confirm who has a Pro membership when an order is placed.

Hope this helps your understanding of it.