Note in this story that these materials were being kept at a farm supply store. While they probably have the licenses and facilities for storing fertilizer and certain flammable gasses, whether they had the same capacity for several tons of sodium and chemical slurry is not clear (can't find more detailed information on them).
Also note that he had shipped 41 pounds of sodium through ebay. I'd say that the issue isn't so much that he mislabeled his shipments once or twice, but rather that it happened again, and again, and again, and someone took notice, followed up on the guy, and turned over just how much material was involved.
Note here that he paid for the storage of the materials by trading 2,000 pounds of borax, which makes me question if this was so that the farm supply store wouldn't have to make an accounting of the storage.
My point in this isn't to say that I think the Government ought to be sticking its nose in everyone's business. But the commerce clause EXISTS FOR CASES LIKE THIS. These ARE things that the Federal Government should regulate. We established the EPA because schmucks were improperly storing hazardous materials and people were getting sick from leakage and rivers were being fouled. We established endangered species protection laws because hundreds of species of plants and animals went extinct because no one said, "Hey, you can't do that."
They are treated differently. The maximum penalties for dumping toxins in a water source are significantly higher -- and the dumping crime also allows for prosecution for other crimes as well, such as assault, homicide/manslaughter, etc.
I agree that the relevance of the first link to the gp's argument is unclear at best. The second link is pretty good, and indicates that false labeling of imports was involved.