You are right PHP and node.js are both normally used in the same way. However, there are some projects and come approaches where both are used at the same time, that's why we pack them together.
As I said in the previous point we have focused in offer the best experience out of the box, so we pack Apache and Php together in the mean stack.
In a lot of production environments is usual a configuration in which Apache act as a proxy for a nodejs application. Using this approach you can serve your application through port 80.
Start your application in your port, for instance, the port 3000.
Go to your /opt/bitnami/apache2/conf/bitnami/bitnami.conf and add the following lines within your default Virtual Host configuration. It should look like this:
ProxyPass / http://127.0.0.1:3000/
ProxyPassReverse / http://127.0.0.1:3000/
Now, you should be able to access your application at http://your-ip/