For the custom-builder of either primarily drop-ins or complete lights, who by nature are likely very particular about every element of the build, eventually the refinement of emitter placement techniques, the addition of alignment augmentation devices, and good old repetition, steady hands, and patience will result in a very high quality result. Otherwise, again by nature of the custom builder, their product wouldn't leave the workshop.
For mass production, I'll assume the process is mostly automated, at least for reflowing the emitter to the MCPCB. Also assuming all other aspects of production have met tolerance standards, I would think the occasional malalignment is just a matter of statistics. That's the nature of mass manufacturing and the need for tolerances.
For those of us that swap emitters, or make our own drop-ins, that don't have the same level of resources as the others, speaking for myself at least, getting proper alignment requires practice and testing new ideas, or sharing in others successful techniques. To loosely paraphrase what Gene Malkoff told me, "you just have to get started and be willing to make mistakes. It's in the failures that you really learn what works and what doesn't". In following this advice, I developed a rudimentary bench top set-up for reflowing that allows me to follow manufacturer recommended procedures such as pre-heating, ramp-up, placement, then cool down.
Cree"s "Soldering and Handling Guidelines" is a wealth of information to help develop "home-made means" to a properly aligned emitter. What I put together for the reflow process cost around $100-$120, more than half of the total was for a magnifier lamp to compensate for deteriorating eyesight.
So how much is tolerable, well that all depends on the individual. Honestly, until I started reading the thread in the LED sub forum regarding this topic, I never even thought to look. In fact I still haven't as I write this. Every light I own seems to provide the expected beam of light, so I've had no reason to consider there was any issue. However, looking at the head-on photos I've seen on here of emitters that appear to be "off-center", I can understand how that would bother some. Undoubtedly, there will also be a direct correlation with tolerance of perceived imperfections, and relative cost of the offending product.
What should be accepted, again depends on the tolerance of the individual. As a recovering perfectionist, I can honestly say that as long as the projection of light is unobstructed, then I'm good to go.
As to your last question Nick, my answer is no. If such would be an issue for someone, I suspect checking the alignment of the emitter will happen the day they get their new light. Even if it doesn't impact the light's performance in the least, if an individual prefers to send it back to the source for refund or replacement, that is certainly their prerogative. Who am I to suggest to another what's good for them, other than my children of course.