Program start by application server means that the RFC server program will be run on the same machine as the application server. In this case, you have different application servers of an SAP system running on different networks connected via SAProuter.
It is posssible to start an RFC server program by a SAPGUI on a workstation which is connected to an SAP application server. This application server has two networks:
one for the network with all SAP application servers and
one for the network with this application server and the frontend workstation with SAPGUI.