Having soot on the bottom of the pot probably has little effect on efficiency. It might help. It is more of a sign of low air intake in the burner system. However, that is the way that many alcohol or Esbit burners operate. I expect to get a little soot, especially if my cook pot is holding very cold water at first.
You can always experiment with the distance from the burner to the pot. You could be able to change the amount of soot. Then you can work it whichever way is best, depending on whether you are shooting for minimum fuel use or fastest boil time or something else.
I will suggest that if you are starting from a standard Ti-Tri Caldera with a standard 12-10 burner or gram cracker burner, then you are already somewhere around a _normal_ compromise point.
–B.G.–