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answer my own question, this seem to work
vpcSgId := cluster.EksCluster.ApplyT(func(eksCluster *awseks.Cluster) pulumi.StringArrayOutput {
            return eksCluster.VpcConfig.ClusterSecurityGroupId().ApplyT(func(sgId *string) []string {
                return []string{*sgId}
            }).(pulumi.StringArrayOutput)
        })

However this doesn't help me in the following case when an input expects pulumi.StringArraryInput.

as vpcSgId in this case is type of pulumi.Output (it is a nested output), why cannot it automatically flatten the nested Output when passed as an argument to another resource creation?