Ain't no such thing as two identical wood basses. Different chunks of wood are going to respond to finishing, string vibrations, etc. differently. Play the two basses side-by-side unamplified to eliminate the effect of different PUP windings, electrical tolerances, etc. on the sound you hear. That's the natural sound of that particular bass. I'm assumng of course that both basses have the same sets of strings that have the same amount of playing time. And that the pickups are adjusted exactly the same. Otherwise, you've thrown a lot of other variables into the equation.
Sorry, but after 30+ years of playing, working on, repairing, "upgrading (though most changes are NOT upgrades), and selling solid body electric instruments, I find that wood is the single most important item for getting a great sound. If it ain't in the wood, no amount of hardware, string, and/or electrical changes are going to make it great. You might make it better, but if the sound ain't in the wood, I just get another instrument now. It's cheaper (both time and money) and it's less frustrating.
jte