The thing is, we already have good tools for process management in UNIX-like operating systems. We have cron, process supervisors, systems for log handling. If you need a separate container for every single process you run, you need to get rid of all the standard UNIX tools and start from scratch. The alternatives for docker-style world do not exist yet and where they exist, they are far from stable. So you will end up reinventing them and most likely do it wrong.
I agree with most of your statement, except the part about "good tools" and the assumption that it will be done wrong forever. Mistakes will be made, but current nix tools aren't really anymore ready for the distributed paradigm.
What I meant is that the current Docker-based solutions are often done without much experience. I'm certainly not against experimenting, but I think that that there are many benefits of running a containerized environment and LXD takes the pragmatic approach that can be used right know with the tools everybody knows.