You should live next to a dog food factory or a bunch of chicken houses. Things don't have to be dangerous to create a situation that you don't want to be living next to.
The net result of relaxing zoning would be more residential housing built, not industrial. Industrial parks around the united states are sitting fallow while housing is being bid up to the moon. Demolishing houses to build a dog food factory would be very unprofitable since you would be replacing high value land use with low value land use. What you are saying is not a good argument for strict zoning, because your hypothetical scenario isn't realistic.
Zoning mistakes have also resulted in the death of vibrant neighborhoods. Having mixed residential and commercial zoning enables things like grocery, corner and hardware stores that make a good place to live even better.
Zoning shouldn't be able to limit how high containers are stacked. If the facility operates in a safe way consistent with OHSA laws, the municipality should come in with a half baked zoning law that prohibits an otherwise reasonable operation from working effectively.
In my travels I have found that many communities across the US seem to generally fear use of height. I've always found this odd compared to rest of the world. Maybe it's just because land is cheap, but it does tend to mean that zoning laws, which try to codify standard practice, do end up overreaching on this particular issue.