I think you're right when you say probably not many people use it. Best bet - submit an issue to them and ask why it doesn't work, if they can give us a clue as to what we should do I'll be more than happy to give it a shot.
Just FYI, I don't do anything magically special on the new ACP. Went for a very clean and basic look so its unfortunate it doesn't work on this browser.
This clearly needs to be documented well and easily found. The usage message of ./nodebb setup --help should indicate the expected syntax and strikingly point out config.json is the wrong syntax in this case to be fed into ./nodebb setup.
In the long run, there should be no special case or different syntax between node app --setup and ./nodebb setup.