I know this sounds strange but we have a feature which we would like to only be installed if the user explicitly selects it from a "Custom" install and not if they select "Complete" or "Typical".
In order to achieve this you can go in the Organization page, select the feature you want and check the "Install based on condition" option for it. Then, in the "Condition" edit box write a false condition (i.e. 1=2).
Let us know if this helped, otherwise give us more details about your scenario.