Author here - the reason is pretty underwhelming: These are the parts I had on hand when I decided to start on the project. Using a chip with a builtin Ethernet peripheral would definitely make more sense (though I'd be trading any complexity of configuring the W5100 for the complexity of configuring STs peripheral). The networking code already abstract the actual chip itself into a driver interface (think read/write/ioctl), so porting the code would be pretty straightforward.

I'll look into the STM32F407 for the main series. Thanks