How is SC16IS740 programmed?
Your problem is due to a misconception, you claim that:


  Practically, I cannot place W5500 on the communication modules because it outputs 2 differential signals, thus requiring 4 fiber optic cables.


But this is not true, standard Ethernet (10BASE-T, 100BASE-TX etc) uses differential signaling over twisted pairs to lower interference, two pairs of the four available to be exact. One pair to transmit and one to receive. Differential signaling means that the wires in each pair carry the same data but inverted polarity. Wikipedia has an article on the subject.

But doing stuff in the physical ethernet layer is not trivial, may I suggest you buy a pair of Fiber Media Converters instead? That way you can design "nodes" with a standard ethernet connection and use optical fiber when necessay using only "off the shelf" stuff.

Also you might want to consider wireless which is much cheaper than optical unless the fiber is already in place.

Oh I almost forgot the original question! SC16IS740 is a UART with and SPI interface (slave). It is not (nor does such a component make much sense) an "SPI-to-UART converter". How one goes about "programming" it I have no idea but it obviously needs a master (your microcontroller) that is programmed to interface with it. Microcontrollers commonly have UARTs built in these days so I don't really see much point in using one anyway.

Best of luck!