When you use zip deploy, the code will run directly in zip (that is mounted to wwwroot folder thus read only). More technical details here

https://learn.microsoft.com/en-us/azure/azure-functions/run-functions-from-deployment-package

If you don't want to use zip deploy, you need to deploy all code into wwwroot using normal deploy method. By just set WebsiteRunFromPackage to 0 won't work as there is code in wwwroot folder yet.