It's an electric instrument, so the only sound that matters is what comes out of the jack.
Absolutely. But the difference in the loudness and quality of the clanking noise coming out of the amp when fretting vigorously is different beetween the two basses in a similar way to the unamplified sound in the air of tapping the necks. Makes me think that it's more likely some property of the neck itself than of, say, the frets or the strings themselves.