Ok, so after playing both guitars unplugged for the past several days I think I have the tone difference mystery solved.
All things being equal (new strings same brand/gauge, pick, string height, neck relief, room, etc.), the neck on the Natural has a more snappy tone similar to a maple necked Strat, where the Trans Gold has a warmer tone edging towards a Rosewood neck tone. I confirmed this by swapping the necks. My ears definitely like the the warmer tone better. Probably because I have two Strats and a Tele that already have the snappy maple neck tones.
All things being equal (new strings same brand/gauge, pick, string height, neck relief, room, etc.), the neck on the Natural has a more snappy tone similar to a maple necked Strat, where the Trans Gold has a warmer tone edging towards a Rosewood neck tone. I confirmed this by swapping the necks. My ears definitely like the the warmer tone better. Probably because I have two Strats and a Tele that already have the snappy maple neck tones.
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