These custom attributes are currently not directly accessible by the profile card in Microsoft Graph hence why you run into this issue. You will likely need to lodge a feature request for this. Here is the link - https://developer.microsoft.com/en-us/graph/support
As a work around, can you try and access the attributes using this below since I see it is available as part of the OnPremiseExtensionAttribute but this depends on whether there was an on prem entity
GET https://graph.microsoft.com/v1.0/users/{id}?$select=onPremisesExtensionAttributes