When you run launchctl list as a normal user, it lists Launch Agents running in your user session; to list Launch Daemons, run it as root (i.e. sudo launchctl list).
More details: some of the launchctl subcommands allow you to explicitly specify which domain you want to deal with. For example:
launchctl print system # Prints Launch *Daemons*
launchctl print user/501 # Prints Launch *Agents* for user #501's session
But the older "legacy" subcommands, like list, load, unload, start, stop, etc predate this convention and use the user ID the command runs as to determine the domain to act on. So for example:
launchctl load /path/to/plist # Loads the plist as an Agent in my user session
launchctl list # Lists Agents in my user session
sudo launchctl load /path/to/plist # Loads it as a Daemon in the system domain
sudo launchctl list # Lists Daemons in the system domain
Your package is presumably running its scripts as root, so it will load the job as a Daemon (which is what you want), but it can depend on exactly how the package is configured.