Hello,
First off my recommendation is a current workaround to what I think is the optimal option. I am following up with the team to see why you are not able to select the top level component and align it together, much as it sounds like you were expecting.
One way you can align the entire component and sub-components is to use the Rigid Group command. What this will allow you to do is use an align on one of the components faces and it will move the entire group of components. If you don't want to keep the rigid group you can then delete the rigid group after the align, and the components should keep the position.
You can either create a rigid group in the subcomponents in their own design or in the design with the block in it. If you create the rigid group in the subcomponents' design you will have to update the file, but your change will persist to other designs for that component. If you create the rigid group in the design with the box, the rigid group is only specific to that design.
The other option though it may require additional work is to leverage joints to lock in the position of components. What you can do is create the joints for your components and connect them together. This way when you move one of the components the rest of them move as expected based off of your joints. Then when you align one of the faces to the box the rest of the components will move as well because of the joints.
Hope this helps, if you have any other questions please let me know.
Cheers,

[Joel Palioca]
[Software QA Engineer]
Joel(dot)Palioca(at)autodesk(dot)com
Autodesk, Inc.