For a new tank, the answer would be stiffeners are not allowed for this purpose. The contract with the tank builder should be reviewed and if it is clear that they owe the owner an API 650 tank then the owner is well within their rights to insist on the contract terms. The owner is entitled to a properly designed, fabricated and erected tank that meets the tolerances of API 650. The quality of the raw material, shop fabrication and the skills of the erection crew should be enough to make a round tank. The vendor is responsible to honor the terms of the contract and comply with API 650.
If after careful and in-depth review you have absolutely no choice, my suggestion would be to remove the stiffeners from the inside, smooth the attachment areas, test via magnetic particle. Then measure the deviations in those areas before, during and after the hydrotest.
If the tank remains out of API 650 tolerance you have to decide if it really matters to you. If after thorough review of design, operations, maintenance and performance expectations it does matter, add seal welded stiffeners to the outside of the tank where they can be observed over time.
Be aware that as the tank is filled it changes shape and as it does this there will be restraint at the stiffeners which means there will be stress concentrations, especially where the stiffeners end. I would not put stiffeners in the bottom course because the bottom course changes shape the most from hydrostatic pressure. Upper shell courses may change shape from wind. All courses may change shape from foundation settlement over time, seismic events, etc.
If attempted, this whole process should be defined, refined and agreed to by all parties in writing, with present and future (warranty) costs addressed and agreed. There needs to be careful thought into why the deviation matters and if adding stiffeners does more harm than good.