Why input/output ground is different and connect them by 0.1 ohm resistor?
The purpose of the 100mohm resistor is for current sensing on pin 16 for the purpose of current limiting. Putting the IC ground on it as well causes the IC's current consumption to be added to this.



TI's document SLVA001E, "Designing Switching Voltage Regulators With the TL494", shows combined grounds on page 24 (above). Whether this represents an error on ON's part is up for debate, but keep in mind that the IC's power is supplied independently from the high voltage and not from the load side of the inductor.