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Jaco didn't remove the pickguard. He removed the bass.
Anything that goes on the wood, including the finish can conceivably affect the sound.
But to what degree? The PG difference could probably be detected by a really good ear, or lab instruments, but not appreciably.
What really interests me however is how most opinions on the matter are either A) pure conjecture; or B) the results of empirical tests subject to Expectation Bias.