The GAE cron is fundamentally just a scheduler for HTTP GET requests:
A cron job invokes a URL, using an HTTP GET request, at a given time
of day. A cron job request is subject to the same limits as those for
push task queues.
A cron job will invoke a URL, using an HTTP GET request, at a given
time of day. An HTTP request invoked by cron can run for up to 60
minutes, but is subject to the same limits as other HTTP
requests.
You cannot directly invoke plain/regular python scripts from the GAE cron itself, see Google cloud app.yaml cron.yaml for python script not working but no log.
But you can invoke such scripts from inside a valid GAE cron handler (if they meet the respective GAE restrictions). The scripts would be running on GAE, though technically flexible environment GAE is really GCE under the hood.
If you want to keep the scripts running on GCE as they are now you'd need a way to trigger them from GAE.