My theory on that is that when people go into the physical stores, they don't see this bundle because in 90% of stores it is hidden behind a counter, or in a drawer, and only people who specifically know about the bundle or search for it online know of its existence. In my opinion this is why it has dropped to $20 (first from 40 to 30, then from 30 to 20) with many copies still available.
However, if they throw away the packaging and just have the game left, they can put the game on a display shelf and the sales will probably be better for the game.
This is all just conjecture, but it seems plausible. Of course we know about this, but random person going into store looking at games won't ever find out about it if it's sitting in a drawer. Not saying it's cool or anything (throwing away the plushies!), but oh well...