One instance (window) is helpful if you want to create a playlist by simply clicking on your files in the file explorer. This way is verified to work in Ubuntu:
Hit “Tools” and then “Preferences”,
Now hit “All” in the “Show Settings” Tab. Go to “Advanced” and tick “Allow only one running instance” and “Enqueue items to playlist when in one instance mode”.
Close VLC and start it up with a file. Your files will now enqueue in the playlist instead of opening a new window.
Here’s a picture of the menu tree: