I'm not fig, but yes - compensating volume thru the amp (mostly) preserves the sound. Running volume at less than 100% kills some highs (and output) at the source and nothing can add that back in... But then again, bumping the volume on the amp may sound slightly different anyway, depending on the amp and your ears...
If you prefer warmer tones, then you may want to hardwire some parallel resistors to mimic the sound of the bass with three pots. Or, you can play around with different values - a trimpot (or a regular pot under the hood) would allow adjusting the resistance actually, if you wired it as a rheostat.
And, if I'm following correctly that you prefer your tone knob closed (ie darkest setting?), then you can also play around with different value caps to see which one you like the most. Or, if I misread and you prefer tone open (brightest sound), then play around with caps to see if you might like a different one