Actually, it doesn't really throw off the breeding chart efforts.

What I've generally seen with the Magic Fish of Mutation is that the mutations are fewer than what you see when using the Unknown Chemical from the store. Out of an entire tankful of babies, you might see only one or two mutations - for instance, one of the babies might have a different fin type. The interesting thing about the mutations that you do get is that, when you examine the mutated fish using the Species button, it will list the parents that would have produced that offspring - not the actual parents that produced the mutated fish. So, if you're keeping track of breeding results, that can be useful information.