Is there a way to pass an array of ports to the setup process ?
some thing like this node app --setup -port="[4567, 4568, 4569]"
Is there a tutorial how to make the NodeBB into an app with notifications?
I don't think there is. You can get some help for making NodeBB an installable PWA here - but I haven't tested it to see if notifications actually work.
Edit: I found this Android app template, but it's not supported by it's author anymore and apparently at least a little broken on Android versions above 8.