Yes, Jacob finds Sam in both AUs. But to say that these two storylines are the same would be saying that Brothers Apart and Brothers Together are the same because Dean found Sam in both.
Brothers Found is placed in 2005 just like Brothers Apart. The storyline of these two will be similar. Sam is out in the rooms trying to find food for his family and he gets caught, only instead of Dean finding him, it’s a complete stranger, an unsuspecting, seventeen year old Jacob Andris.
Brothers Unexpected is placed in 1993, the same week of Sam’s curse. He is ten, and runs away from Walt and Mallory Watch. They can’t get to him before he gets caught by a young Jake, who is only four-going-on-five.
In other words, they are completely different plots and completely different style stories. If they were the same, we wouldn’t write them. Just like we shouldn’t write any more Brothers Together if it was the same as Brothers Apart, right?