If your inventory sits too long in their warehouse, the fees go from "regular" storage fees to "long-term" storage fees. Those fees are much higher, which incentivizes the seller to put the stuff on sale to blow it out of their warehouses, or you can have the inventory sent back to you.
Also, fees vary by category and season. Around the holidays, you'll see them making a push to increase long-term storage fees to make way for the stuff that will actually sell, and on categories which are hot for the holidays, you might see them providing incentives with lower storage fees.
I'm not the primary person that deals with Amazon FBA, but he sits next to me. Don't take what I'm saying as the gospel, but this is based on somewhat second hand experiencing and reading some of the emails that come through. My partner pays more attention to those details.
That assumes equivalent costs in other parts of your operation. But with FBA, isn't Amazon doing your stock-keeping for you? You can avoid paying for warehouse space if Amazon is your warehouse.