I guess you still need to do more training in network topology. Understanding network topology comes with regular study and experience of which when lacking can through one into confusion.

Now to the topology, you should be able to differentiate between physical and logical topology.

Physical topology show how the devices are connected to one another physically bearing in mind all interconnecting switches. Physical topology can be said to be Layer 2 topology. But logical topology will only shows you from IP addressing point of view or how they communicate with each other. In another word L3 perspective.

The diagram here is logical topology showing where ip addresses are assigned base on their subnet. It show how R3 communicate with FW. But between them is a switch through which the interfaces are connected. Because the switch function is not L3 function it is seen as transparent.

Here R3 f0/0 is connected to a switch port whose port is in vlan123 while FW F0/0 is connected to the same switch or it may be another on a port with the same VLAN 123. Although physically they are connected to switche(s) logical the can communicate with the switch transparently passing the traffic. Here there is not direct connection between R3 and FW. The same apply to FW F0/1 and R2 F0/1.

If this confuse you let me know where things get more confuse maybe I will have time to explain further.

Cheers..