The first exclusion
On this page11
The definition of weight
"The term 'weight' as used in connection with any commodity or service means net weight. When a commodity is sold by drained weight, the term means net drained weight."
So weight means net weight by default
Not as a special case for packaged goods. Any time a commodity is sold by weight, the word already means net.
And net weight is defined by exclusion
"The weight of a commodity excluding any materials, substances, or items not considered to be part of the commodity."
With a list
"Containers, conveyances, bags, wrappers, packaging materials, labels, individual piece coverings, decorative accompaniments, and coupons."
Containers is first
Which is not an accident of alphabetical order, and it is the sentence this entire property exists for. In a refill shop the container is on the scale, and the law has already said it is not part of what is being sold.
The list is not closed
"Include, but are not limited to." A lid, a gasket, a pump, a label the customer stuck on themselves: all of it is the customer's and none of it is the commodity.
There is one carve-out and it is about services
"Except that, depending on the type of service rendered, packaging materials may be considered to be part of the service." The example in the handbook is shipping, where the weight of packing material is part of what is being paid for.
Which does not reach a refill counter
You are selling a commodity, not a shipping service. The packaging is the customer's own and they brought it with them.
Why this is easy to get wrong
Because the obvious way to run the counter is to put the jar on the scale and fill it until the number looks right. That number includes the jar, and the customer paid for it.
The fix is arithmetic, and the next page is about it
Weigh the empty container, record it, subtract it. The whole of compliance here is one subtraction done consistently.