If one had dozens of guitars made of the same wood species, of the same wood thickness and with the same bracing but half of them with bolt-on necks and half with glued necks; you might be able to draw some conclusions about how the different attachment methods affect sound. Otherwise, there are so many variables that any conclusions or assumptions are meaningless.
Most of the sound that the guitar amplifies comes from the vibration transmitted by the bridge. The extent to which the neck transmits audible sound to the soundboard would depend on the phase relationship. If the vibration from the neck is out of phase with the sound at the bridge, then improved neck joint transmission would have a damping effect. If the sound is in phase, then improved transmissio might have a positive effect. The point is that assumptions are being made in the absence of enough knowledge of how the whole guitar works to amplify string vibration.
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