But would they then be looking upside down?
I'm guessing the Andalite brain could cope with that, and figure out how to get the image right-side-up. Humans have that ability to some degree, actually. I heard about a scientific study where this guy wore glasses that were made to turn everything that he saw upside down. After about a day, his brain was able to compensate, and things looked right-side up again, even though the image was still actually upside-down. Then when he took the glasses off, things were upside down again.
I would speculate that Andalite eyes would work the same way, but on a much quicker scale. Because they would probably get turned every which way, no matter what mechanism by which they operate. Andalite brains would have to be able to adjust for that.