You bring up apples and other orchard fruits. Yes, in production you want things like uniformity and yield. But from a long term survival standpoint, you want some diversity, such as through preservation of heritage varieties or allowing some seeds to grow and selecting from them. Otherwise, you end up with a very short list of possible options when faced with new diseases. You need some genetic pool to select resistant rootstock from. It also prevents things like genetic and epigenetic adaptations to the environment (see progressive cold hardening). Of course the economics of it discourages farmers from selecting currently inferior varieties for crops. But perhaps a biosecurity program could fill that gap.