ronsimpson,
Thank you for such a great explanation. After digesting it a little I fully understand what is going on. Due to the fact that there is no easy way for the LTC3873 to sense the voltage output it is creating by pulsing Q1 on and off they have to come up with a feedback to the chip. They did this elegantly by using a current mirror to create the 1.2volts across pin 3 and 4. As the -5v output goes too high or goes too low due to load change, this will change the 1.2 voltage to go higher or lower, which then tells the chip to adjust it's duty cycle to the FET accordingly to maintain the constant -5v.
Again, thank you. The drawings you made helped a ton. Much respect.