I was attempting to do filtering on a custom UPS property, but it looks like the org chart is not pulling the custom properties from UPS. Is this accurate or is there something I can configure to allow it to select the custom properties as well.
Actually, it's possible to use the data from User Profiles custom properties in Org Chart.
Once a new User Properties is created (SharePoint admin center -> User Profiles -> Manage User Properties -> New Property), please follow the same steps as for adding managed property for dotted manager to make the new property searchable.