I was trying version 5.0 out yesterday and came across a similar issue.
5.0 forces you to have the settings file. But the default settings file has a row:
This becomes a problem if you run the application and use -f to point it to a custom configuration file like this.
sudo /usr/share/logstash/bin/logstash -f /home/ec2-user/logstashfileinput.yaml --path.settings /etc/logstash/
Whatever file you point to using -f gets ignored and instead uses the file located at /etc/logstash/conf.d/. Assuming there even is one. The settings file takes precedence over whatever you pass in as a command line flag. If you were already planning on using that file then it isn't a problem, but for my cases I wasn't.
I haven't tested it, but it's possible that whatever is in the settings file would also take precedence over -w and -b too.
It probably won't affect anything on our production machines, but it's a bit annoying when I am trying to quickly test different configs.