I would think that the Miller ghost that the protomolecule uses to interface with Holden is a perfect example of it being changed by the process of outcompeting. The interludes in Cibola burn are a very good example of how despite still functioning the protomolecule has been permanently changed by what it did in Sol system and the humans it assimilated in the process

If i had to guess I would say it likely comes down to how the rice and bean plants fair in low G. If they're eating real rice and fake beans I would think its because the rice is either grown on or near ceres as well as the yeast and fungus substitutes that make up the fake beans, whereas real beans would have to be imported in

While possible I think the relative acceleration and maneuverability of a ship constrained by human passengers compared to a missile means that you can point your drive plume at it but the missile will already be programmed to come in on an arc intended to avoid the plume and with its better maneuverability it will still be able to hit its target effectively.