pufferpanel VS mscs

Are you asking for a pannel? If so there's a few good ones; i personally recommend 3. 1 being AMP 2 being ptero and 3 being puffer. Their all really useful

I've been looking into this recently and up to now I only tried Puffer Panel. It should have some of the things you want including accounts that can only access given servers and custom Cron jobs per server. It leaves some to be desired like the ability to update servers more easily and because of that I've been looking into maybe also trying Pterodactyl or Easy-WI.

I'd take this to the puffer-panel team themselves https://github.com/PufferPanel/PufferPanel/issues/new/choose

I've always run pufferpanel on Ubuntu server (no desktop) for my minecraft instances.

With that said pufferpanel is an.excellent starting point

Ideally, I'd like something like the Minecraft Server Control Script. Something that makes setting up, backing up, and restarting servers pretty simple. As well as simplifying the process of running multiple servers.

I personally use https://github.com/MinecraftServerControl/mscs to manage multiple servers on one physical server.

For running the server take a look at https://github.com/MinecraftServerControl/mscs It makes it relatively easy to get a server running, restart it automatically if it crashes, make backups and can even start mapping tools.

Start a farm of Minecraft servers. There's a well- and constantly-developed server management script on Github called MSCS that makes it surprisingly easy to manage servers externally via command line.