No, you're right... they would not be making money in that scenario.
Merchandise is offered wholesale to retailers by manufacturers based on graded markups. In the past there was an "A B C" designation for these pricing schemes, and while I'm not sure this is still the structure they employ (it's been a lot of years since I've been in the manufacturing business), the idea still holds.
Spend some time cruising around the GC/MF sites, and you'll notice an interesting thing. The "full retail price" is always listed, followed by the discounted price. On some items (Fender products, for instance), the difference is pretty startling. This is because these items are on an "A markup," which means that the average retailer is paying the manufacturer 50% of the suggested retail price. A volume retailer like GC/MF that buys boxcar-loads of items is probably paying around 45%, which allows them to offer what seem to be ridiculous discounts. Other manufacturers are on a tighter margin (B and C markups), which only discount to the retailer in the range of 20-35%; EBMM basses are a good example, as you will almost never see a new one priced at a discount of greater than 30% off the MSRP. Still other manufacturers offer no discounting at all... in these cases you'll note that the GC/MF price is usually a dollar less than the MSRP (and you'll notice that nobody is able to offer a price outside of a very tight range... this is very noticeable with boutique pedals, for instance).
Under no circumstances is GC/MF buying product at less than 45% of the sticker price, and even these situations are relatively rare. So if the price you pay drops below 50% of the MSRP, they're losing money. If it's something like 25% of the DISCOUNT price (what they normally charge for the item), they would be taking a major bath.
Now, you might be delighted to know that GC/MF is taking a major bath. But you should be honest with yourself about what that means to their pricing/marketing as a whole. Other consumers will have to deal with smaller discounts as they scramble to make up for the losses they might experience from multiple discount purchases that resulted from a software glitch.
And of course there's the whole issue of honesty. I mean, if an offer for a discount states "not to be used in conjunction with any other offer" and you find a way to use multiple offers to your advantage, this IMHO amounts to a form of stealing. Some people may think that stealing from the "evil empire" is okay. I frankly do not, and this is why I did not attempt to take advantage of this situation. Cuz you know John Lennon was right... instant karma IS going to get you....