Is it permissible to supplicate for the deceased mother and for all deceased Muslims at her grave, or is supplication restricted to the mother only?

You are permitted to supplicate for your mother at her grave or away from it, for all of that reaches her. Similarly, you are permitted to supplicate for her within the general supplication for the Muslim deceased in that graveyard. If you supplicate for her individually, and then supplicate for her within the general supplication for the deceased of the graveyard, this brings more reward for her.