They are having certain set of differences.
The App Engine flexible environment has the following differences to Compute Engine:
Flexible environment VM instances are restarted on a weekly basis. During restarts, Google's management services apply any necessary operating system and security updates.
You always have root access to Compute Engine VM instances. By default, SSH access to the VM instances in the flexible environment is disabled. If you choose, you can enable root access to your app's VM instances.
Code deployments can take longer as container images are built by using the Cloud Build service.
The geographical region of a flexible environment VM instance is determined by the location that you specify for the App Engine Application of your GCP project. Google's management services ensures that the VM instances are co-located for optimal performance.