I used to be involved in some intermediate gunsmithing work, and we had these tools called 'dial calipers' which have a little gauge you read and you can measure extremely precise things. We used it for getting cylinder diameters or clearances that needed that degree of precision.
I can only imagine that in aviation, there are even more advanced tools, especially with a well-respected corp like Boeing.
I would think also, that when there are these clearance issues in parts, part of the concern that makes it worth raising flags over is the fact that it's consistently off amongst different aircraft. If someone were to bring me a rifle that had some important gas clearance off, I wouldn't be that concerned, just do the work and get it back in the field, but if guys are bringing me the same rifle with the same issue over and over, it makes me really uneasy because it's inefficient for my shop, and it points to carelessness from the vendor, which raises suspicion when dealing with orthogonal issues from the same vendor.
If these flapper bushings are bad consistently, and they had a spec and didn't meet it, what other corners did they cut?
Just my two cents. I don't know shit about aviation, but I can appreciate the systemic concern.