The graph on the left shows how the measurement accuracy changes with the sensor resistance value. A lower reference resistor value gives better accuracy in the lower sensor resistor range, and for better measurement accuracy at high sensor resistance a higher value reference resistor helps.
The goal of Vinduino is to help with irrigation management, so we are not really interested in high accuracy when the soil is totally soaked or bone dry, beyond the point of permanent plant wilting. We need best accuracy at the target soil moisture level. With this data in mind, my choice is for using 4700 Ohm, as this gives good accuracy in the most common soil moisture range. With the described sensor design, 100% moisture gives a sensor value around 300 Ohm, at 50% soil moisture the sensor reads 1 kilo Ohm. Refer to the Vinduino sensor calibration blog post for more details.
Whatever resistance value you choose for the R1 and R2 resistors connected to the sensor, should be declared in the software code. So for using 4k7 Ohm resistors (4700 Ohm), the Arduino code should be changed to:
const long knownResistor = 4700; // Constant value of known resistor in Ohms
For ultimate accuracy, as resistors usually come with a tolerance of 5% or 1%, you can measure the real resistance with a multimeter and enter that as known resistor value.