If you grow 2 strains together as mothers in a room for like 5 years one sativa and one indica, they will eventually end up on the same flower cycle and start to resemble them selves. I think because the environment is highly controlled, the process speeds it's self up. I have seen that happen. I have even heard that eventually one will Hermie in flower, but have never seen that.
This is why instead of keeping moms, I just take fresh handful of clones from the previous girls, and keep the healthiest few.
Yes, they are responding to pheromones and hormones, but the plants that acclimatize outdoors, are obviously the ones whose expressed genes are the ones that give an advantage (for example, not losing your flowers to mold, or flowering earlier as a male).. what you're seeing expressed in those plants that change are not new mutations, they were always there, but the environment didn't favor them..
Anyhow, we're both on the same page I think