Not sure what you mean by "app builds" here. The container process is in a user namespace, not docker itself and "docker build" will work just fine. Maybe you are referring to something else? Let me know, would love to take a look.
Layers are largely an implementation detail in Docker. Yeah they are there, you can even check the sha of them, but not something users interact with. I don't think I've personally heard any of tbis confusion except for very old versions of Docker before content-addressabity and the concept of layers did leak through (each layer was an "image")... maybe there's still some lasting confusion here? I could see this I suppose with things like older books/blogs/etc referring to them as a first class citizen. They are definitely not and certainly should not be. One of the early design mistakes which are long since corrected (docker 1.10 introduced content addressable images, and the concept of the image as a whole rather than an image being a tree of other images).
Also, a side note, "docker run --init" gets you the init you are looking for, can set it as default in the daemon as well.
Note, I've been a maintainer/contributor to Docker for 5 years now.