LOL, you just disproved your own point with that image.
How? My point is that the sensor should be enlarged to 6000x6000 in which case there's no penalty in terms of resolution in any aspect ratio. Photonut's post was rather confusing so might have misunderstood. Particularly the part about vignetting.
But there are penalties in terms of performance, contrast, veiling flare, complexity and cost.
The camera needs to be designed with the assumption that you might use all of the pixels on the sensor. Increasing the pixel count requires faster hardware, or slower overall performance.
Sensors have a mirror-like finish. Some of the light that hits the sensor reflects into the camera and introduces veiling flare. Obviously, we need to let light fall onto the pixels we want in our final image. However, anytime we are not using pixels, we have a mirror-like surface, and no advantage. This could be addressed by having an adjustable matte black mask that would move to cover the parts of the sensor not being used.