For me the power of docker is its inherent immutability. I want to be able to move a service around without having to manual tinker, install packages and change permissions etc. It’s repeatable and reliable. However, to get to the point of understanding enough about it to do this reliably can be a huge investment of time. As a daily user of docker (and k8s) I would use it everyday over a VM. I’ve lost count of the number of VMs I’ve setup following installation guidelines, and missed a single step - so machines that should be identical aren’t. I do however understand the frustration with it when you first start, but IMO stick with it as the benefits are huge.
In most cases you can get away with over mounting configuration files within the container. In extreme cases you can build your own image - but the steps for that are just the changes you would have applied manually on a VM. At least that image is repeatable and you can bring it up somewhere else without having to manually apply all those changes in a panic.