Nothing so complicated as that.
The point is that if the Chimp genone is 10% larger than the Human one, then it isn’t possible that there is less than a 5% difference in the two sets.
If I have 100 coins, and you have 110 coins, it is impossible for stack of coins to be 95% identical, because even if they are all pennies, your stack will have 10 pennies where I don’t have any, and will in fact be 10% different from mine.
Whether that distinction has any real VALUE in the discussion is another question entirely.
Those differences (in counts of the same gene) have to contribute to the computation of raw difference in genomic structure.