Why Magento 2 Setup/Uninstall Script ONLY deletes modules installed through Composer? I am not able to understand the reason behind this!
Composer and Magento are two different tools. Magento uses composer, but Magento does not make use of composer functionality. So when you delete a module in the context of Magento, it is correct not to remove it from the composer.json.
It is just not the purpose of the command.