Gamedatalibary doesn't include digital sales, I'm guessing GDL took this figure from Nintendo's official numbers which include digital.
Due to shortages Animal Crossing New Leaf actually did extremely well digitally for a 3DS game during its launch.
At beginning of June AC NH Had sales of 4,7 millions in retail. If that chart from June 4th is to believe, AC NH was at 1,1 million in digital sales. That’s 20% of the total sales.
If you add 20% today, AC NH should be at 6,3 millions in total sales.
Should reach Pokémon green/red by the end of the year and break the record.