not sure on the import, but how are you using the texture in the material matters.
a VT cna possibly sample differently then another texture.
linear color, color, Grayscale, etc.
Of you made a texture object parameter and you pass it off to a function, or into the Tex field of a texture sample, you have to match the texture sample type to the correct texture type.
This means that if you have a normal you can’t replace it with a diffuse in the material instance without getting errors (And its a good thing, since otherwise the rendering would be off).
Not sure if thats whay is happening for you, or if it helps any.
As far as the rest. I have VT on and when I import TGA files they work fine without automatically becoming VTs.