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Its still unclear to me why this issue only presents when running on linux, maybe the helm process returns faster. Waiting for cert-manager to start + 10 secs fixes it though, waiting for cert-manager alone still results in failures. The bottom issue is some form of deadlock on the tls-secret object, where cert-manager is unable to update because the object was modified while cert-manager was running.
Other cleanup:
Create namespace was unnecessary.
process.StandardError.ReadLineAsync() was occasionally throwing exceptions, process.OutputDataReceived += new DataReceivedEventHandler(OutputHandler) seems to be better.