> So if a gene/allele gets moved to a different place, it still counts as no difference.

Definitely not. Translocation often leads to or implies different expression of genes. As an aside many, many translocations over large amounts of evolutionary time can lead to things like chromosome loss and/or speciation events. These are important forms of genetic change/mutation that do lead to important functional change. And they do make genomes quite different in ways that aren't measurable by simple percentages.