I think that it's related on the output size you select. If you want a precise final size, then calculations are more accurate, and require a double pass to encode video with the best quality.

The main "defect" of autoGK is that it lacks of some flexibility. If you want more control on the encodig process, and then a less "automated" software, you need to use GordianKnot, also free.

I tried time ago GordianKnot, but I found it rather complex to use, not so intuitive like AutoGK. But I'm not a video expert