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GKE does the creation of the VMs and setup of them, joining them to the cluster and applying labels for example.

The specific issue appears to be about creating new "node pools". Creating standard VMs in GCP works fine however, so this is specific to GKE and their internal tooling that integrates with the rest of GCP.

GKE doesn't (at least to my knowledge) allow you to create VMs separately and join them to the cluster in any kind of easy fashion.

It's actually not just GKE, there have been issues creating normal VMs since late Friday night. It seems anything that required creating VMs gave back resource exhaustion errors. I finally got a cluster for us-east1 setup last night so it looks like the resource issues are clearing up though.

Nope, GKE = master/control plane owned by Google. Customers are just tenants, who can schedule workloads.

GKE gives you a fully managed Master Node.