Each node in a Molecule will listen for web service requests. Since each node listens, it is up to the caller to decide which node to send requests to (each node will have its own IP address).
When you configure the shared web server settings, you are configuring it for the entire molecule.
Even though only one host is displayed in the UI for that Molecule, the requester could in fact send to any of the nodes in the Molecule.
For example, if we have hosts A, B, and C in the Molecule. The Shared Web Server Settings say that the Base URL is http://A:9090. Even though the Base URL only references server A, the requester could actually send to http://B:9090 or http://C:9090.
Typically, rather than have the requester decide which node to communicate with, a load balancer would be used to distribute requests to each of the nodes. This load balancer is external to the Atom and the implementation is up to the molecule owner. You can set a load balancer up to listen for all inbound traffic - you will need to have the requests be sent to a different URL to hit the load balancer.
The load balancer will then route the traffic to each of the three nodes within your Molecule. If you have server A, B, and C each hosting a node, you can route the traffic to http://A:9090/...,http://B:9090/..., and http://C:9090/....