Perhaps the term "flat spot" is being used to describe any irregularity that produces a thump as the tire rotates. It might be a bulge rather than a flat spot. Belt separation or some failure in the carcass leading to bulging can have the same symptoms as a "flat spot" except it usually doesn't dissipate much as they warm up. Flat spotting from sitting is mostly associated with the old bias ply tires. I have lots of radials that sit for many months and ride like new when taken out for a spin. One of my boat trailers has bias plys and they can thump a bit until they warm up if they have sat idle for a month or so. But it's nothing like some of the nylon corded bias plys back "in the day".
This sounds to me like the dealer is on a fishing mission. Flat spotting from sitting would be obvious to the user, not something that could only be discerned by a mechanic inspection.