Gates on chips are essentially precise marks.

In metal machine shops there are apparently certain things you do all at the same time before you move the parts around because once you move them you can’t ever get them in exactly the same spot again - due to tolerances in the tools.

If for instance you want to grind a precision bolt out of solid stock, you slap an oversized piece of bar into the chuck. If it’s slightly off-center it doesn’t matter. If it’s slightly skewed it doesn’t matter, because you’re going to grind a (nearly) perfectly straight section out of the middle of the bar, and at exactly a 90° angle to the chuck. Then cut the threads.

And then, you’re going to take the bolt out of the chuck, and use a different tool to cut the head of the bolt. But it doesn’t matter if the head is four thousandths of an inch off of dead center of the bolt because it’s just a surface for the tool and a surface to spread the force of the tension in the bolt.

Which is very similar to the idea of building a bunch of chiplets and putting targeting marks on them at the same time, then putting those chips into a device that slices them up and prepares the surfaces for assembly.