How to automatically patch EC2 instances created from CloudFormation Stacks using SSM patch manager

Hello.

CloudFormation drift checks differences in AWS settings (instance type, EBS type, etc.), so drift does not occur with information inside the EC2 OS.
https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/using-cfn-stack-drift.html

CloudFormation detects drift on those AWS resources that support drift detection. Resources that don't support drift detection are assigned a drift status of NOT_CHECKED. For a list of AWS resources that support drift detection, see Resources that support import and drift detection operations.