When a Spirit uses a special rule to make a sacred site with only one Presence (e.g., River Surges in Sunlight using River's Domain in a Wetland), do they count as having two Presence there?

When a Spirit uses a special rule to make a sacred site with only one Presence (e.g., River Surges in Sunlight using River's Domain in a Wetland), do they count as having two Presence there?

No, they still just count as having as many Presence as they have disks in the land.
Similarly, when an Incarna counts as a Sacred Site, it's still just counts as one Presence.
While two Presence is enough to make a land a Sacred Site (as suggested by the iconography), the reverse is not true.