Nothing is actually rendered on the pre-render scanline, though?

As far as I understand it, the missing cycle at the end of the pre-render scanline means that the first scanline will start a cycle early every other frame. When this happens, that scanline will be drawn one pixel to the left of where it should be. In practice, this typically causes the first few scanlines to get skewed slightly (you can see this at the top right corner of your Mighty Bomb Jack screenshot) but I don't know enough about NTSC decoding to explain why this happens. This is more noticeable if you can get footage of the system displaying tiles on the top of the background, rather than the plain blue background at the top like your Mighty Bomb Jack screenshot has.