Layers are interesting but they are still maturing and have hard to detect bugs and incompatibilities [1]. The more layers the worse it becomes so they can add management overhead. Containers and layers are separate technologies so its useful to leave it as a choice.
The benefits have also often been oversold. For instance reuse, all container platforms provide a library of base OS images. These can simply to used as required instead of trying to use layers. How many upper layers are there going to be on top the base OS that can be reused? This sounds good as an idea but often does not pan out, usually its just the base OS or base OS plus dev environment being reused so why use layers?
And If there are updates to any of the lower layers for instance security or version updates usually the container needs to be rebuilt so again you are not benefiting from using layers to build containers.
Using it at run time like you would run a copy of a container to keep the original intact still makes sense, but using it to build containers adds a lot of complexity and management overhead.