Hi @Error_401 ,
It sounds like your mixing IaaS, the deployed VM, with PaaS, Azure App Service. MySQL InApp; which you can read more about here, is an offering meant for quickly testing/troubleshooting your application before moving to production workloads. Since MySQL In-App is scaled down local database, connecting to it is done in the app service through various dynamically created application settings; it doesn't use 3306
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I can't speak on XAMPP, but you can follow https://learn.microsoft.com/en-us/azure/app-service/tutorial-php-mysql-app?pivots=platform-linux tutorial on creating a PHP app backed by MySQL Azure instance. You can leverage the MySQL In-App to perform all your testing and then export the schema to a MySQL Azure instance.
Regards,
Ryan