Recently Robyn Mercurio, a violinist and descendant of Patrick Porter, provided me with the following link to some fiddling by Tom Jarrell, in which he explains why rattles were put into the violins:
If nothing else, this shows that this particular idea has broader application than to the Porter violin. It is clearly a common folkway story. Tom explains that in the time before there were "city violin cases", people hung their violins on the wall; spiders would get into them and weave their webs. Given the tight openings into the body of the violin it would be hard to get those cobwebs out of the violin. Shaking the violin with the rattles in there would perhaps "cut them out".
Tom notes that some folks think the rattles are in there to "improve the sound". Tom's explanation seems the more likely...though if someone didn't know why this was done, perhaps "improving the sound" would seem to be the only obvious explanation---even if it didn't really make sense. A "Just So" story.
Perhaps this is an example of how there's often a core of truth in folk stories---mangled beyond recognition, but there to be recognized if you get the right "key".