There seem to be some rules around custom attributes being available for use in a query and in plan views. Is there a way to add those attributes?

Hi,

Custom attributes should be visible while creating a new WI query. Make sure you create the query after you have added & saved the custom attribute in the process configuration, otherwise it might not show up in the list. There's also a check-box labeled 'Show custom', make sure that's enabled.

In order to have custom attributes show up in plans:
Go to Process Configuration -> Project Configuration -> Configuration Data -> Planning -> Plan Attributes. In the Attribute Mapping section, add your custom attribute.
Now select a plan and click on Edit View. Under the View Layout tab, your custom attribute should show up. Move it to the selected section & save.

Hope this helped!

How to sort an Iteration Plan Work Item List by a custom attribute: 
http://www-01.ibm.com/support/docview.wss?uid=swg21446901