Biomass Mutation overwrites any effects that set the power and/or toughness of a creature you control to a specific value. Effects that modify power and/or toughness but don't set them to a specific value (like the one created by Giant Growth), power/toughness changes from counters, and effects that switch a creature's power and toughness will continue to apply. For example, say you control a 1/1 creature that's getting +4/+2 from an Aura, has a +1/+1 counter on it, and is affected by an effect that switches its power and toughness. This creature is 4/6. If you cast Biomass Mutation with X equal to 4, the creature would become 7/9 (4/4, +4/+2 from the Aura, +1/+1 from the counter, then switch power and toughness).