How to set custom DNS in GKE Autopilot

Question

I run Composer 2 in Autopilot mode and I need to setup custom dns server for some domains in GKE Autopilot. In GKE Standart (non autopilot) i can simple change kube-dns configmap to add

stubDomains:
    {
      "domain.com": ["9.9.9.9"]
    }

but in Autopilot i can't change any resources in namespace kube-system. Also I created Cloud DNS but pod doesn't resolve domain name through it.