Can you actually prove what your saying about dumping the seconds on discount stores?
Read through some of the horror stories here on peoples experiences...lopsided bowls, missing glaze, holes, tank covers that were twisted and warped so they wouldn't sit flat...any company with any sort of quality control would never have them leave the factory. More than one person opened more than one box before they found one acceptable on all pieces. No manufacturer can stay solvent making really crappy products, so hopefully rejects are a small percentage of their output. Empirical evidence points to the big box stores accepting anything off the assembly line. The vast majority of them are good, but the (slightly) bad ones make it through because they aren't caught. One reason why the same toilet at a plumbing supply store may cost more, another is their volume; a plumber can't take the time to replace a defective toilet - a big box store purchaser may not recognize a defect, or think they're all like that, and the store and buyer become the QA group. Any less than perfect ones the homeowner doesn't bring back is more profit for all rather than having the factory destroy it.
Important note - I'm not a pro
Retired Defense Industry Engineer; Schluter 2.5-day Workshop Completed 2013, 2014