Why voltage at AREF is given by Vin * R2 / Rtotal In chapter 4 of Arduino Workshop on page 85 (or page 31 in the pdf) it says that the voltage at AREF in the schematic is given by: 

Vin * R2 / (R2 + R1)

However, the voltage is flowing from 5V to Ground so isn't AREF actually in parallel with R1, and so shouldn't AREF be given by:

Vin * R1 / (R1 + R2) ?
You are correct.

$$V_{ref} = \dfrac{R_1}{R_1 + R_2} \cdot V_{CC}$$

or Vref = Vin * R1 / (R1 + R2) until we finally get MathJax enabled on this site.