Synchronize ACM and non-ACM instructions

[jlewi]

The way we configure Kubeflow when deployed with ACM has diverged a bit from non-ACM instructions.

For example, with ACM instructions we

• Run kpt functions to remove the namespace for non namespace resources
• Use istio-system/ingressgateway (to address kubeflow/manifests#1169)
• Structure the manifests according to ACM structured repo

There's no reason we couldn't do all of the same steps even when not using ACM. Only difference would be in how we apply the manifests.

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