That's not a flawed model for them, because it is exactly their plan. By producing a limited number of games that are only available at a certain time they are creating a market and demand. If they produced too many people wouldn't want them.
There would be no difference if they did it as pre-orders, because that is basically what they are doing now. If they do not set a specific amount of unit to be created they could find themselves in a situation where it actually costs more to produce the units that they bring in - this is because the manufacturing is done in bulk. They have to purchase a specific amount of units from the factory - and this is very likely linked to the 6,000 or so units that they usually produce. A number that I'm sure has been arrived at by crunching the numbers by determining how many can they make, while meeting the factory quotas and not sitting on too many unsold units for too long.
So, if they were to open pre-orders, per your suggestion, and they receive 6,973 orders. They can't just produce that number. They likely have to buy them in specific multiples - whether it's 6,000, 8,000, 10,000, etc.. Even if it was 7,000 that's still 27 unsold units. Why do that when they could ensure that they sell all of them by capping the number at 6,000?
Like sworddude said, if the demand is there, they will make more. If they aren't making more it just means that there isn't enough interest for them to justify making another 6,000 units.