I have seen a lot of posts to the MDT forum recently of people trying to get applications selected or checked in the wizard based on the task sequence that is selected. The common thread is that they define the applications in CustmSettings.ini using the TaskSequenceID property and, while that does in fact install the applications during the task sequence, they are not checked in the wizard to show that they will be installed.
The reason for this is simple. CustomSettings is evaluated before and after the wizard, but not during. When it is evaluated before the wizard, the value for TaskSequenceID has not been set yet, so the Applications property is not populated and no applications are checked on the Applications pane.
What we need to accomplish is to have the rules file evaluated after a value is set for TaskSequenceID. See my blog post here for a solution to this question.