The Toolkit doesn't document or make visible the mechanism for doing this, because it's currently unreliable - in most cases it will get the same answer as the SQL Compare UI, but there are certain cases where SQL Compare will get it right and just the Toolkit alone will get it wrong.
The mechanism for playing with dependancies is as follows:
There is a method of the Work class called Work.SetImplicitlySelectedDifferences which takes a Differences object and sets the dependancy flags appropriately.
In each Difference object within that Differences object, there is a boolean field called 'SelectedImplicitly' which is meant to tell you if an object has been selected as a dependancy.
However, these have both been made deliberately invisible so that people don't rely on them, as there are quite a variety of cases where they will give out misleading information.