Here is another data point: I happened across VIN 131 yesterday in a parking lot in my area. I checked the headlight enclosures and both of them were within about 2mm of being flush with the bumper (by eye and by feel). They were symmetrical.
So it is possible for Tesla to get the headlights flush with the body. I suspect most owners don’t notice the issue and therefore do not request that Tesla rectify it.
As it happened, there were two other Model 3s in the same parking lot! (No, this was not the Tesla factory, headquarters, a showroom or a service center, it was a retail establishment). Their headlights were not flush and were asymmetrical, which is what I usually see.
And during the 30 minute drive from my house to the parking lot in question I saw four Model 3s on the road. They are becoming a common sight in the San Francisco Bay Area.