Modyfing app.yaml in a way you did disables only one type of healthchecks, there are the backend ones still running and they are not accessible with app.yaml configuration. There are two issues created in Google's Issue Tracker related to this topic - you can track and/or star them here and here.
What you can do is modifying the healthchecks via Cloud Shell to make them less agressive. Deploy a version with the healthchecks enabled (if you have them disabled right now) and list them:
$ gcloud compute https-health-checks list
For viewing the current settings of the given healthcheck:
$ gcloud compute https-health-checks describe [healthcheck_NAME]
Change the settings for the healthcheck with the name ending with "-hcs":
$ gcloud compute https-health-checks update [healthcheck_NAME] --check-interval=5 --healthy-threshold=2 --timeout=5 --unhealthy-threshold=2
(obviously you can choose different values in the command above)
You can find the above commands in GCP docs here.