Many people seem confused about the role of rootstocks, especially in light of regenerative systems. Each cultivar, whether one used for roots or for fruits, has it’s own varied genetic makeup, and is chosen for certain traits. When we are given the opportunity to make a two cultivar (grafted) plant we have the luxury of choosing a variety that has special traits for one or the other purposes. In stone fruit there are a few varieties that are good at both (Lovell peach, for example), but generally very few have that ability. The downsides of grafting are almost always less than the downside of using the inferior genetics of a fruiting cultivar as a rootstock. For question #1, the two cultivars (root and fruit) may have different exudates but the differences are minor. #2, plants have an innate ability to heal so what may seem like an injury will no longer be much of an issue once they are fully grown. An example of various genetically distinct varieties growing together is seen through root grafting, where a plant will grow closely to another plant of the same species, and when the roots meet they will grow together naturally. In orchards a virus or chemical exposure (herbicide for example) may spread in this way. #3 that is true that crown gall can be an issue but that is more of an issue innate to the species than to the location of the graft. I have seen high grafted walnuts still get crown gall, and one can obviously see root galls below ground in areas that may have been damaged but are not actual grafting sites.