Heating an intake doesn't generally heat the air pulled into the cylinders much. All it does is heat any fuel droplets that hit it and re-vaporize them, keeping them from condensing out of the intake air stream.
However, drawing intake air from under the hood instead of outside does make the intake charge hotter and you will notice a small power differance.
It is just fine to heat the intake while pulling in outside air, it isn't counterproductive.
