Until you get into the Tier 4s, the mutation will always change the Tier for either the flower or foliage, so if you start with a common plant you are likely to get a higher Tier, or the other way around.

The advantage of mutating before pollination is that you can then self-pollinate the plant to save a copy of that seed. But sometimes I'll mutate afterwards if I just want to do some experimentation or recover from a pruning gone bad.