How can I make Photoshop's transparency 'checkerboard' match with pixel size?
There are only 3 options for Transparency Grid size in Photoshop:
They do not conform to a pixel standard like you're thinking of them. They transmute with the display size. For example set to large on a 50px by 50px image when viewing it very large on my display gets:
Zoomed out without any other changes however gets us this:
As you can see the number of "squares" representing transparency is not constant.