I ordered 10 things from the big A... all items said they were coming from them, all said they were in stock. All free shipping. So far I've gotten one shipping notice per day, for four straight days. In other words... So far they have shipped 4 individually, and there's still 6 to go. And they bill individually, so it's probably going to take 15 minutes just to sort the mess out on my statement. Then I ordered from another place, and they shipped 39 pieces in one shipment, and the 40th piece just two days later. And the one piece is a dimensional rate, like the other 39 pieces, so it is the max shipping rate. I doubt they made any profit at all. Then another place sent me half an order, then the second half just two days later, even though I said it was OK to wait and do the whole thing together.
One obvious explanation is your assumption that their shipping rates are the same as yours and mine. They probably get ground rate discounts of 15-30% and air rate discounts of ~50%. Or from the carriers' point of view, why wouldn't you do a cost+5% deal to Amazon that's a $100 million a year account for UPS. What's UPS's incremental cost of having Amazon's account, when UPS has the entire distribution network already set up? That's how A does it.
Never said I assume they pay the same. Of course A gets a giant discount. But wasted money is wasted money. So far they've spent 4 times what they could have, whatever the rate is, and that will go to at least 5 when they send the rest.