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Dynamatt does not not stop rattles, it lower's the resonating fq of the panel it is applied to. The Dynamatt in the boot isn't really achieving anything.
If you didn't fill the service holes i reccomend cutting the section of dynamatt out and filing them. Even with the service holes filled and no dynamatt in place in that area, would still sound better than the alternative.
Asking a dumb question (because thats what im good at ), what should he be filling them with?