Hi @Andrew Badgley,
I can see the use case for needing to limit the categories to a smaller subset when displaying the chart, particularly in the case of something like Tags or Owners. It is unlikely that the Custom Chart App would be updated to accommodate this as the apps are built on older technology.
As we are actively building and enhancing our new Custom Views feature, I would recommend submitting this feedback for the Custom Bar/Column Chart widget.
In the meantime, you can access the custom chart app code in the public RallyCommunity github organization and tweak it to accommodate your scenario. If you did this, you would need to install the app as a Custom HTML App (rather than the Custom Chart from the app catalog).
I hope this helps!