Your model is bad. (Never follow a bunch of loopy calculations until you check the model. Garbage in, garbade out and all that.)
Why do you assume that the 99 percent similarity means man has grown 200 genes that chimps lack? Your model concedes--even as you yourself do not--that chimps and humans diverged from a common ancestry.
Recall that the humand and chimp cytochrome c DNA differ by a single base pair. Is that difference averaged into the 99 percent overall figure?
You might as well say that the number of organs in the body is 220, so man has 2.2 organs that chimps do not. The 99 percent difference does not refer to the number of genes, but their content. Your model assumes it refers to the number of genes, assumes man and not chimp has to make all the new ones, assumes the content of said genes has to be lucked out from scratch . . . (Pant! Pant)
Bad model.
99 percent similarity. A sloppy post, but I trust the message is not lost.
Because otherwise man and chimp would have 100% the same genes. And no, if you knew a little bit of biology you would not say that the gene where one part was different is counted in the above. All genes for similar functions in different species have differences between them. That is why the blood of different animals cannot be used for transfusions in each other. No the 200 genes (or 300 or 700 if the higher numbers said by some to be in the human genome) are totally different. That higher species have new genes should not surprise us. The simplest known bacteria has some 500 genes. Therefore a lot of new genes had to have been created from the time of the first life to now. Let me remind you again how long it would take to just make one gene in man using the most favorable assumptions towards evolution a 1 with 42 zeros behind it years.