For
Question/Example 1:
Use:
(Parent.Milestones.Name = "Milestone_2")Notice the .Milestones reference is on the 'Parent' of the object you're targeting. If you're targeting Features then this Parent refers to the Initiative. You can then change the drop-down of your target object in the app to Initiative and then this query will refer to Themes.
<Please see attached file for image>

For
Question/Example 2:Use:
(Parent.Parent.Milestones.FormattedID= "MI456")Notice the .Milestones reference is on the 'Parent.Parent' of the object you're targeting. If you're targeting Features then this Parent refers to the Epics..
<Please see attached file for image>