I believe the way it works is:
You (the brewer) pay federal excise tax on the manufacture (in barrels) when it is drinkable (finished, carbonated, usually measured in the bright tank). You pay state excise tax (by the gallon) on the packaged product (bottle, keg) unless you sell the package to a distributor(bonded), in which case he is responsible for the state excise tax when it it sold to retail. If you self distribute, then you the brewer, are responsible for the state excise taxes when the beer is packaged.
The brewers in this case are just trucking soup!