Wow, you and
@mongo are asking me hard questions now!
Re acoustic forces at launch I had not not considered them acting directly on the ship tiles due to the height of the booster and the deluge system being below the ship. However indirectly the acoustic loading will add to the 'vibration' being transmitted up the booster to the ship.
Re transonic flows, these can be a little chaotic but the point I am trying to make is that the flows and loads that will be seen will not be dissimilar to those on other rockets and hence SpaceX should be fairly confident of their prediction accuracy (lots of analysis codes have been developed for combat aircraft which have more complex geometries and where test data has been available to validate the correlations used). So while the design work needs to be done the answers should be close to reality.
The upper atmosphere flow and heat transfer (convective and radiative) modelling just seems to have far more uncertainty to me. The first flight should remove a lot of that uncertainty.