The tax calculation is done the way it is because that's how the New York tax law specifies that it should be done. It's not a question of right or wrong. The New York legislature can structure the tax calculation any way they want to. There is no requirement that the tax laws be fair or logical, and different people have different ideas about what is fair or logical.
They are calculating the percentage of your income that comes from New York State sources. Both the federal and New York amounts used in that calculation include only income that would be taxable by New York if you were a New York resident. That seems reasonable to me, but that's just my opinion. You may disagree, but it's still what the New York tax law requires.
