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Hello Kishu,
You are right to point out that “Environment Variables” can be set in the Flex environment only as outlined in the document shared by my colleague earlier. Under the Standard environment a user has no control on the JVM or any ability to modify the runtime environment. If a user needs more control he/she needs to use the Flexible environment to have more control on the JVM. See the following link to see the differences between Flexible environment and Standard environment.
Choosing your App Engine environment
However if you need to use the Flexible environment, you do not need to migrate your entire app to the Flexible environment. Instead you can create a micro service under the Flexible environment to serve your needs. Your existing service running in the standard environment can call the other services using HTTP, Cloud Tasks alpha, or Cloud Pub/Sub. Please see the following link for details.
When to use the flexible environment