Speaking of which, I question the idea that Stax is extensively changing or even tweaking these production lines. I work in a similar business. While we're not as small as Stax by far, my product is the best scientific instrumentation in the world for this particular application. The devices are expensive ($100k), small (handheld), and specialized. I've also worked in similar industries so have experience in these kinds of production lines.
FIrst, it would be very unusual for a company to change an existing line while in production, for several reasons.
Motivation: there is none. Extensive R&D has gone into the existing design, who in their right mind would want to mess with it while trying to get product out to customers and make bills? Another way to say it, "don't mess with your cash cow"
Difficulty: it's called "changing the airplane engines while in flight". Any change has potential side effects that only show up over time, who would do this on an existing production line?
Staffing. R&D is always tasked for the next products, why revisit what is working and selling, and who has staff for that?
Cost. Small production lines are expensive. Suppliers only want to do one, simple thing. Changing and making variations costs money and time. Certainly some things like coatings are not changed, except for necessity or good reason. Additionally it would be unlikely there would be great variation across the products for the basic components like film and coatings, it's too expensive (another topic would be production line design, which is how to create a myriad of seemingly different products that are actually just small variants of each other)
Change sells. In other words, say you figure out an improvement, why would you give it away for free and unannounced on the existing line? You'd be crazy to do this, what you'd want to do is create a new product and trumpet the improvement.
I've never seen it at any company that anything changes in production except for bug fixes, and reluctantly at that. Now note I'm not arguing whether people are hearing some kind of variation with the existing production line, but it's highly unlikely they've actually changed the line. If it is true, then it's highly likely to be sample variation.
And if that was true, I'd say either Stax has poor control over production (seems unlikely), or that the headphones are so difficult to manufacture that there is an inherent degree of variability (this happens frequently, such as with silicon). And if that was true, the variability wouldn't be systematic, but instance based. Meaning a batch of headphones from one day would all be different. Systematic variation would have to be due to something like what the humidity was when they made the headphone (just an example, Stax appears to assemble in a 'near cleanroom' environment).
Edit: I'll add that I happened to work in Japan for years in this industry, so have a sense of how the Japanese electronics industry works. Production engineering is mostly the same world wide, but for a Japanese only company like Stax I'd opine that it would be extremely unlikely for them to do this. Japanese companies are very conservative in this way, only the Germans are their equal.