Unfortunately, you cannot do that using projects. Projects share the same Node-RED instance including the settings.js file, useDir and installed nodes.
However, it is fairly easy to have multiple Node-RED instances instead. That gives you completely independent settings, nodes, etc.
In fact, if you look at my alternate-node-red-installer repo on GitHub, you will find something that may help.
That will create you a master folder, install node-red into it, create a userDir (
data) folder in it, make sure that settings.js exists and creates a package.json file with suitable npm start scripts. It is cross-platform.
The only thing it currently doesn't do is install node.js for you and it doesn't create a systemd script (for auto-running on Linux) since it is cross-platform - one day I hope to add that as well but it is quite complex as it needs to know about user ids.
Once you have used the script twice to create node-red instances in two different master folders, you can change the settings.js to adjust the ports and any other settings you want to.
You can even have different versions of node-red running simultaneously this way - though my script doesn't cater for that itself just now. However, you can just use the script as a guide for doing your own installation.