Disclaimer: I'm not an expert in Cilium! Only recently got into reading about it because of Jessie Frazelle's tweet about it. Still planning on deploying it into my small homelab.

It's my understanding that Cilium chose to do it this way because it allows low-level control of each network namespace that containers launch in, in addition to a high-level view of the system from the k8s API. This allows Cilium to build firewalling features that operate at a different level -- iptables/nftables filters on IP addresses and ports, but Cilium can filter on k8s resources and L7 protocols.