Prescale is used for making pixels look less blurry when no shaders are active (making the filtering less obvious when upscaling the emulated output to the full resolution of the used display), I don't think it will have much (any?) effect with HLSL, crt-geom, etc. Scanlines (or rather, the used mask) will always stay in their proper positions unless something goes wrong.
What do you mean that the Channel F "quadruples the scanlines"? Do you have any pictures of this effect on real hardware?