Tim,
If you call the things by their proper names there is nothing illogical on that.
Tone controls change the frequency response of the system. Cables, or some passive components change the perceived sound in a different way, that can not be explained by our usual measurements, but sometimes suggest a change in the sense of what we perceive by using a tone control. But, unhappily, no tone control can add the extra perceived resolution, detail or musical sense given sometimes by what you properly designate by tweaks.
Perhaps I should reformulate - what is a tweak?
Some may consider it a "tweak" but in the case of part replacement including caps and resistors we tend to call this an upgrade or possibly a modification to the circuit or component. But, upgrade would probably be more correct.
Rich