An alternative may be to create a repository and merge the configurations, but the yi packages should use the yii container which already depends on other yii packages.
It is not yii-web outside of the framework. It is different PSR container with Yii.
If I understand that but in yii packages using another container is not going to guarantee that the package works completely since it depends indirectly on the implementation of our container
I think optional container is a good way to increase the frameworks audience. Some people are really like containers written by the League and Symfony. It will be difficult for them to understand how to use functionality of factory or subcontainers in our implementation. And they don't need to if they can use what they used to use before. So I'm for container-agnostic libraries.
Если предполагается, что пользователь сможет заменить контейнер на любой PSR-совместимый, то в компонентах нельзя использовать фишки, которые есть только в Yii DI контейнере.