Does k3s' bundled flannel backend support CNI plugins like multus? We weren't able to quickly figure out how to use multus with the flannel backend but were able to disable it and run flannel in the cluster with multus.

no, all it supports are the packaged backends. As of recent releases you can provide your own flannel config, but most people just disable it (--flannel-backend=none) and deploy their own CNI from scratch.

Thanks for the confirmation Brandon.