I solved it thanks to @Adam, via support ticket. Like @Aliysa_Enhance said: If you want to make it work on a subdomain you need to add that subdomain as a separate site.
Once you have it as a separate site, you need to add (in Enhance) an A or CNAME record for this new website in main domain.
Once you verify the A/CNAME is resolvable, you can proceed to configure node.js. The only thing I struggled with was the "working directory" configuration: it has to be relative to the $HOME folder. So I placed my node app directly in public_html folder, and my app needs to start from the "server" subfolder. So I set the working directory as "public_html/server". Then added "npm start" as Startup Command.
Then click on Deploy App and you should see in the log to the right that it will install the necessary packages and start the service.
Here's a screenshot of the working subdomain configuration:
