Any changes in the contract requirements usually qualifies as an "extra" and that translates into money paid by the "owner" for the changes requested.
Hoppers, bunkers, silos, etc. can be welded to AWS D1.1 requirements and internal piping can be used as structural supports. Piping doesn't necessarily mean a liquid under pressure is to be contained in the pipe. The pipe may be used for any purpose, including the the movement of air or solid materials, i.e., grain, sawdust, sand, etc.
AWS does not require every pipe weld to be a complete joint penetration weld. The extent of welding should have been specified by the drawings or other contract document.
If D1.1 was specified by the project specifications or the by the drawings, and the owner adds the requirements for NDT other than visual inspection, the owner is responsible for the cost of preparing the material for the NDT, the cost of NDT, and the cost to make any repairs as a result of deficiencies identified by the NDT. The exception is if the owner can prove the fabricator was attempting to defraud the owner.
On the surface, your description of what took place sounds like there was a "failure to communicate" the project requirements to the fabricator. The suggestion that you go back to the beginning is sound advice. You need to find out what the original requirements were (in writing) and what changes (in writing) were added by the owner after the contract was "signed".
It is difficult to meet the customer's expectations if those expectations were ill defined to begin with.
Best regards - Al