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Very good diagnosis. We are also using Kubernetes, but using a NodePort service and an annotation that keeps a route53 DNS record updated with current backend worker nodes IP addresses. Once we scaled beyond 512 bytes (around 34 nodes) all of our backend servers configured with server-template and those DNS lookups started failing with the 'MAINT' status. It took a while to finally figure out what was happening.
Setting "accepted_payload_size 8192" in the resolvers config section is able to get it to work again.