Why is the sort order significant?
In a meal the duration reactions are limited to ingredients closest to each other in the sort order. Given 3 ingredients A, B and C on the sort list such that A is listed somewhere above B and B is listed somewhere above C, the duration calculation is based on A to B duration and B to C duration. The duration listed for A to C has no bearing on the meal duration.
In multiple layer recipes the last ingredient on the sort list in the higher quantity layer reacts to the first ingredient on the sort list in the next lower quantity layer, no matter their respective positions in the sort order.
See Sort Order Todo for a list of the ingredients that have yet to be placed.
Note: a second level indent just means the ingredient is not a primary ingredient, its position in the order is correct.