I'm no expert but have spent more time than I should on HB...
will try my best to explain what I've digested so far..
Think of coffee grinding as a form of gap grinding. What that means is, during grinding, you bring two grinding discs close together to form a small gap, just enough to allow coffee particles smaller than the gap to pass through. By increasing/decreasing the size of this gap, you can control the coffee particle size you get.
Let's use flat burrs as example to explain the 'alignment' concept.
Imagine you have two round flat grinding discs and you overlay the discs on top of each other. Now, move the top discs up into the air by 0.3mm. If you do it correctly (and parallel-ly), the gap size between the discs should be exactly 0.3mm around the entire circumference. If you accidentally tilt the top discs by a few degree, now your gap will be uneven (say 0.1mm on one side and 0.5mm on the other side). This gap size affects your grind uniformity because as above, the gap size determines your grind particle size .
Another thing that could go wrong - the two flat dics should be completely concentric to each other. Meaning that when the two discs are overlaid on top of each other, you wouldn't be able to see the edges of the other discs when looking from the top/bottom.
These(above) are what is usually referred to as burrs alignment.
Once you have two burrs perfectly concentric and parallel to each other, you need to rotate one of the discs to grind coffee. This is another source of error that can affect the gap size. In case the axis of rotation is not in the center, or a poor motor shaft, your burrs will have run out and that will appear wobbly visually.
Tolerance is just a manufacturing concept. Manufacturing is never perfect. If you order 10 rods cut to 10 cm length, you never get all of them cut to 10.0000 cm. Some of them will be cut to 10.1 cm, some will be cut to 9.9 cm, and many others will be cut to between 9.9-10.1cm. The tolerance is 0.1 cm in this case. In the manufacturing process of course there will be some rods cut to 10.3cm or beyond, but that would be considered a reject and will/should never reach you. Depending on the situation, you can usually specify the tolerance needed (if the application requires 0.01cm instead of 0.1cm). The lower the tolerance allowable, the more expensive it is (higher chance to get out-of-tolerance rejects, and the cost has to go somewhere).
The thing with tolerance in grinder is, there is no universally acceptable tolerance. I recall Versalab has a runout tolerance of around 0.3mm. Mazzer claims to aim for 0.02mm. Frank I think he aims for 0.01mm. But as far as I know, measuring the actual tolerance is very time consuming and very tricky because it has to be measured once everything is assembled (at least for the parts affecting the gap size). Thus it is almost impossible to do it at large scale manufacturing.
Another catch is, because a grinder is made of many parts, the tolerance is the sum of every parts added up together, after assembly
. You can't just measure the tolerance of the rotating shaft preassembly and call it a day. The burrs carrier, the grind chamber, the motor shaft, and the burrs themselves, when assembled together, will all affect the final tolerance.
The gist answer to your question is cost limitation. Low tolerance is possible with the big companies, but it is not practical/economic enough for what the costumers are willing to pay.
To your another question, in theory, you do change the burrs alignment whenever you're taking the burrs out from its carrier. There's some slop to how the burrs can sit in the carrer, if you pay close attention. But it's usually quite minor enough to be noticable. However, if a large coffee debris is stuck on the burr carrier surface, the burr will be tilted and definitely you have affected the alignment. Other than that, if the motor shaft is poorly made, or the carrier is not machined evenly, that'll be out of your hand to correct (in most cases).