According to ZhugeEX, Uncharted 4 bundles were "significantly more than the game sold standalone"
Uncharted 4 would be higher than God of War if bundles were counted.
Uncharted 4 bundles were significantly over 3 million units in the US.
So I would say it's fair to say that 8.7 million copies sold in the US by December 2016 were mostly bundles. This is why bundles are brought up. Even Mat Piscatella had to explain why Uncharted and The Last of Us were not in the top 5, even though they sold more copies.
The Last of Us Part II surpassed Horizon Zero Dawn in July to become the Third Best-Selling PlayStation 4 Exclusive of all time.
No one is calling Uncharted 4 a flop since it made less money than Horizon Zero Dawn, which was a brand new IP.
Also, it's unlikely that The Last of Us would've surpassed God of War in sales, but we know it wouldn't have reached 10 million copies sold in 13 months or 19.5 million in 3 years without bundles.
Units sold are not an indicator of a game's success. I'm sure if The Last of Us was bundled similar to other Sony titles, they would've announced sales figures earlier. So far, The Last of Us Part II was one of the least bundled exclusives from Sony during the PS4 era.