Our entire development environment runs in Docker. To address your points.
That's Dockerfile design, better organisation & forethought into image content might help you.
Yes there is, run your containers with SYS_PTRACE etc.
That's not a negative, but also, nothing about Docker prevents you running a DB somewhere else, or indeed, within the application container at the same time.
We use IPv6 without issue.
Yep, it can, mostly what you're seeing is an OS problem. Run Linux, install docker, and mount /dev (with the proper kernel options) into the container.
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Our entire development environment runs in Docker. To address your points.