I agree. Biodiversity in agriculture is severely lacking. The good news is that we have heritage seeds. However, we don't have the capacity to ramp that stock up quickly. The main issue is that farmers will choose the best seeds for the current conditions/risks. This leads to a consensus winning variety. There's no benefit to the farmer to plant "inferior" seeds for an event that has yet to happen.

A "biodiversity subsidy" sounds like a kind of agricultural-assistance I could get behind, although the devil is always in the details.

One concern that comes to mind: If a certain variation is more-susceptible to a particular disease or pest, and becomes a beachhead or reservoir--fun mixed metaphors there--for infection.

Yeah, this would probably be best served by some biosecurity program at the USDA or a handful of universities.

Reading more, there appear to be just two cultivars naturally resistant to Xylella fastidiosa.

Spain already grows hundreds of cultivars of olive trees, though only three are used for the bulk of the olive oil. So replacing those with resistant ones would reduce diversity.

A different monoculture is not the solution to the problem of a monoculture. Replacing all of them with the resistant ones would reduce biodiversity (perhaps the resistant ones are susceptible to other diseases, perhaps the nonresistant ones will at some point be resistant to a new disease). See https://en.m.wikipedia.org/wiki/Polyculture

The main problem with polyculture being that it assumes local farmers are smart and cunning individuals who find (perhaps unorthodox) solutions in constrained, complex and realistic environments because their livelihoods depend on it (or because they got an interesting idea and couldn't let it go), and who know more about their challenges than random hn commenters like me, instead of being mindless drones that can be replaced/interchanged at will by central overlords with complete control over the panopticon food factory.