Just tried to do 2 sided scanning with my MFC-J4540DW Brother printer. (AUD $329)

Unfortunately this printer doesn't have - 2 sided scan settings option which should appear under Scan Settings in the iPrint&Scan application

To get 2-sided scanning in the InkVestment series you need to go up to a MFC-J5955DW or which is (AUD $599) or MFC-J6955DW (AUD $679) - Check the officeworks.com.au website

This is what you see in iPrint&Scan if your Brother printer DOES NOT support 2-sided printing

This is what you see if you Brother Printer supports 2-sided scanning