Because the vast, vast, majority of those alterations are silent or non-sense modifications? Those 200 bases that get altered in GMO absolutely have an effect, aimed towards a specific outcome. The millions of alterations that occur naturally are random (though distributed according to the conservation-level of the region) and thus far less likely to impact the final product in any meaningful sense.
That said, I'm all for well tested and investigated GMO. If we are to feed our increasing populations, we must increase the yield and efficacy of our methods.