KIND uses kubeadm which is the upstream standard for bootstrapping. It also supports multi masters and even launches a haproxy load balancer for kube-apiserver! K3S uses it's own bootstrapping, as well as non upstream binaries. It also replaces etcd with it's own shim.

Non-kubeadm bootstrapped clusters are snowflakes in my opinion. You will find many docs that will not work with k3s due to missing systemd. You also lose some flexibility. For example there is no way to change the container runtime cgroup driver.

KIND is designed for local use on your workstation. Cluster API is the project to use for production deployments. You can drive Cluster API with KIND for testing though!