@Keennon, Mike - unfortunately many Identity/Azure AD capabilities (dynamic membership, custom token claims, provisioning, change tracking) do not yet support schema extensions. You'll need to use Directory Extensions instead. It's a similar but earlier version of schema extensions but only for directory. Management of the directory extension definitions and extension values is also exposed through Microsoft Graph. See Create extensions.
We're also in the process of writing a topic that compares and contrasts the different extensibility options in Microsoft Graph, along with examples.
Hope this helps.