Routing between internal ports

Sure. Assuming you are subnetting into separate networks (i.e. 172.16.1.0/24 and 172.16.2.0/24), you can assign IP addresses to each interface and the FortiGate will automatically make routing table entries for each interface. You will then need to create firewall rules for traffic in each direction between the two interfaces. The FortiGate has no concept of internal vs. external beyond port labels. You can assign any IP block to any interface and traffic flow is controlled by firewall rules. When you break up the internal switch to operate in interface mode, each port is no different from ports labeled WAN or DMZ.