Yes, this is a problem and it is trying to be addressed by generic kernel images which should make it so that you no longer need to build a device specific kernel as all of the device specific stuff has been modularized.
https://source.android.com/docs/core/architecture/kernel/gen...
>Root support and service managers need to be installed aftermarket using the unofficial solution Magisk.
Root should not be necessary and these break Android's security model. Perhaps there is an operating system API that could be added that could provide the features you are looking for while keeping the system secure.
>No vendor kernel out of the box supports kernel compile time flags to enable the infrastructure to run Linux containers using Docker, Podman or LXC.
Android apps already have their own sandbox. It would be better to develop apps than docker images as darker images don't really follow the Android security model as well. What you want should be possible with Android 13 allowing for kvm.
>Self-invented file hierarchy with a lot of restrictions that make sense from an Android UI perspective but are prohibitive when used as a regular distro.
Why care about a file hierarchy? NixOS does away with it and seems to get along fine. Apps shouldn't rely on it.
>Since Android and drivers use bionic libc, it's not possible to run regular Linux binaries that tap into certain hardware features like Vulkan without reworking and recompiling them.
Most people run apps and not binaries. It is going to need to be reworked anyways.