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The car has 1000's of resonant frequencies, not just one; every little part in the car actually has its own. He locally changed the ones on the wheel well for sure, but it is unlikely that made a big difference on the overall cars modes. What he could have done though is changed the transfer path for the energy which can have a pronounced effect on acoustic response. No one in the automotive sector ever wants to run a transfer path analysis as it is brutal so these are rarely optimized all that effectively. Definitely used for oh shit engineering, but normally it is one of the first areas of NVH that are sidestepped as much as possible.

Do the rear seat backs fold down? If so, is it worse with them down?

You might have changed the resonant frequency of the car so the drone is more noticeable now. I know exhaust manufacturers are now measuring the cars acoustics and tuning the exhaust to avoid drone. But those are on the higher end of the market not flowmaster cherry bombs.