It's not that manipulating tone is beyond us: good makers do it all the time. The problem is that 'tone' is both highly subjective and very complicated.
Your own post attests to the 'subjective' nature of it: other people say your guitar is 'dark' sounding, but you don't hear it as such. Now, it's possible that it would sound dark to you if you were listening to somebody else play it, but there are other possibilites too. For example, maybe you just use 'dark' to mean something else that what your friends mean. Or maybe it's all it the way you play it.
In terms of the complexity; usually, we assume something that sounds 'bright' will have a lot of high frequency in the signal. However, it can happen that, say, a mahogany Dread with very little going on in the higher part of the spectrum will still sound 'bright'. I _think_ that has to do with the sharper 'attack' of the light weight back, but it's hard to say. We might be using the same term to describe a number of different things, or maybe there's more than one thing that you need to have to get 'bright', and you can mix and match different proportions of those things to get a 'bright' guitar.
I have observed that a certain kind of 'coupling' between the vibration of the whole body of the guitar and the air in the box can yeild what I think of as a 'dark' sound. It's not simply that there is more energy i the low end, but rather that the energy is more evenly distributed: there is not one strong note with weaker ones on either side, but rather several notes in the lowest range that are moderately strong. There are other components to this as well, of course.
I make violins as well as guitars, and I would not be too sure that the violin makers would be any better than guitar makers are at defining the things that go into making the sound. I have to wonder if guitar makers are just a bit more honest about what they don't know, or can't describe. I can tell you that there's a lot of disagreement as to what goes into the 'Strad sound', and a lot of effort going into duplicating it. If those guys really knew what they were doing, don't you think they'd have solved that one after all these years?
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