So referees at chess tournaments are not, in fact, looking at a chess board, but instead a checkers board. How can they possibly judge a game of chess then?

If you rotate a chessboard by 90 degrees it's no longer a chessboard, by your reasoning at least.

It's not that the spots aren't circles, it's just that circles blend together very well and become difficult to notice while the crescent shape does not blend well.

If you have a region covered in circles of light, they blend together to look like a relatively homogenous blob of light.

Viruses are the more unique factor here, not being cells and whatnot. Fungus and bacteria are more alike than viruses and literally anything else.