That makes no sense. If you order 2 items, and they're in 2 different warehouses, you'll get 2 packages. They aren't going to ship from 1 warehouse to a 2nd warehouse and then bundle them.
In my experience, they are (if more economical than sending 2 packages). That is often one reason when it takes long to ship.
If you are a FBA seller, you can see these warehouse transfers in the event reports often between a new order coming in ("pending") and the order being shipped.
This is obviously more common with slower shipping options - they won't have a lot of time to combine anything with 1-day shipping.
I've also clearly seen the difference myself as a buyer between the shipping options - if I select faster shipping, the items tend to ship quicker but they are split into more shipments more often.
Also, they may do the same when you order a single item as well - they first move the item to a nearer warehouse and only then ship, if cheaper than shipping directly and if they have the time.
