I agree it is confusing. Personally, I would count it as 3 genes, the same way a person that has 2 BPs and one corn has 3 snakes. You don't say they have only 2 snakes just because 2 of them are the same kind.
But, for whatever reason, that isn't the way the BP community does it. They count the killer bee as 2 genes because it has 2 different types of genes. I guess this is because of breeding potential. A killer bee can only pass on 2 genes to its offspring; it can't pass on both copies of the pastel gene.
On the flip side, if you think of how easy it is to produce a snake, having 2 copies of the same gene does make it more difficult to produce, so in that way it would make sense to call a killer bee a 3 gene snake.
Regardless of what makes sense to you or me, just learn to count the different types of genes so you'll be speaking the same language as every one else.
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