You could create a group (Light Group - Home Assistant) and use that in the card. The controls are always linked to one entity, but with the group that will go to all lights in the group.
edit: should have read better that you already have the groups. I truly don’t know why the difference is being made. But it might be a good idea to test and configure your card separately from the popup first and then copy everything over to the popup settings config. Otherwise check the topic for the light-entity-card: Light Entity Card