Author here (sorry for the late response, I didn't see this got posted to HN). These are all valid concerns (especially about spontaneous diploidization), but

Author here (sorry for the late response, I didn't see this got posted to HN). These are all valid concerns (especially about spontaneous diploidization), but I think they can be overcome with sufficiently rigorous quality control (probably whole genome sequencing, not just genotyping). The issues with epistasis (i.e. will polygenic scores continue to be valid at extreme values) are also worth noting. I think that improved models (besides the linear ones in current use) are likely to solve this though. The hard part is actually doing the meiosis.