When Griffen referred to the annoying sound of the rubber dinghy banging against the boat, it was when she and Wood were sunbathing up outside on deck where the sound would not be muffled by the multiple walls of the boat, only the single wall at the stern. When Paul Miller examined the soundproofing of the yacht, he was probably using the main stateroom as the reference point, since that is presumably where Wood took notice of any sound. Between the stern swimstep and the main stateroom there are at least a couple of walls as well as possibly the engineroom of the boat, providing plenty of material to muffle the rubber dinghy's knocking on the boat.
The only way I'd think that the dinghy would create an annoying sound was if it were to be hitting the side of the yacht alongside the main stateroom. But I doubt this, since the dinghy was seen by at least one witness as being at the stern of the boat, against the swimstep.