In fact, no brands to my knowledge aligns the crowns the correct way up. There are a couple of reasons for this.
First is the Daytona use a Triplock. This has a gasket inside the crown everytime you screw it in, which compresses. Over time as the gasket wears out from multiple screw/unscrewing, this means the crown screws in a different distance over time. Thus, even if the crown aligns perfectly out of factory, it will eventually misalign in the long run.
Second is impracticality. The same argument applies to screws - no watchmaker to my knowledge intentionally manufacture or align all the screws exactly the same orientation. It is simply not practical - lets use movement screws as an example. The threads are turned by a solid die or equivalent, by turning the theads are practically "deformed" into shape, and there is no easy way to control where the starting point of the thread is. Sure, you can thread it first then mill the slots later, but then the movement bridge has to also have perfectly tapped screwholes which is not practical to do. And as you tighten the screw, depending on the strength you are yet further deforming the metal of the threads and it gets quite unpredictable how much you can tighten those tiny screws.
In the case of the Rolex crown, you need to align both the crown, and the inner crown tube, which in turn also has to align to the case its tapped into. Theres so many variables here, including the gaskets, and where the waterproofness function is of more importance than the aesthetical alignment of the crown logo. Maybe a watchmaker can adjust this by using different gasket thicknesses, I am not sure.
In carpentry or woodworking, the term is called "clocking" the screws. There are a few ways to do it - one is you use extra tall screwheads, then after screwing in the screw, you mill off the screwhead flat and machine in new slots. The other ways are for instance, screw it in, note how much angle the slot is off, remove the screw and then remove more material from the screwhole till the screw goes in the correct amount to align the heads. Both ways are again, not practical in watchmaking and are different because you dont necessarily need to service and disassemble carpentry like a watch every couple years...
As a joke, the Patek Aquanaut's screwdown crown has the Calatrava cross which is symmetrical in four directions. Thus it has four times higher chance than Rolex crowns of being in the correct orientation from factory...
Regards,
skyeriding