Comment by cysteinechapel

Such an advantage that is rare and across such long time scales would be so small on average that it would be effectively neutral. Natural selection can only really act on fitness advantages greater than on the order of the inverse of effective population size, which for large multicellular organisms such as animals, is low. Most of this is really just noisy transcription/binding/etc.

For example, we don't keep transposons in general because they're useful, which are almost half of our genomes, and are a major source of disruptive variation. They persist because we're just not very good at preventing them from spreading, we have some suppressive mechanisms but they don't work all the time, and there's a bit of an arms race between transposons and host. Nonetheless, they can occasionally provide variation that is beneficial.