It was a fantastic panel for your own minecraft server hosting on your own dedicated server. I have an 8 cores server running on pufferpanel and 10 minecraft server in it with bungee.
Unfortunately, the panel is very hard to control while the extra ports need to be manually configured and forwarded between dockers through SSH or Scales. So it is not recommended to get this panel to customers while it is still under heavy development. But you can try to launch it on your own server to test it out.
Yep, I run my set up like this right now and it's entirely possible to run PufferPanel inside of a container. I've not attempted Scales, but assuming you map /home to the container it'd probably work too.
I'm very pro docker, but we're also going to allow users to not be forced to use docker in the next upcoming release as well.
@bobdabiulder Please make a thread in the Support section if you have further issues, but I did answer your question. Please make sure you have all of the dependencies listed on https://pufferpanel.readme.io/docs/getting-started including php5-cli otherwise the installer will not work.
You can upload custom jars, just make sure the name of the JAR you upload matches the name of the JAR set when creating the server in the admin area. You can manage plugins through the 'File Manager' tab, and can upload / configure plugin settings there.