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You can definitely write a custom authorizer to do what you want; but doing so takes away the ease with which you can link Cognito and API Gateway now. The custom authorizer will have to determine whether the caller is a user or service and authenticate the access appropriately. So it's more work for you to write that code.
Would you consider having a separate API for service integration? That might be easier especially if the API is already deployed through automation - deploy it twice; use the same configuration except for the authorizer.
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