The reason they are running out of the shotgun is because Dak is apparently only comfortable throwing out of the shotgun at this point.
So they throw run looks out of the formation so as to not be predictable. It's another reason why I find it funny you day don't give Romo the job back when he is healthy and then you turn around and complain about a huge limitation in the offense due to a Dak weakness.
Romo is one of the 7 best quarterbacks on Earth. If he's healthy you play him. Why? Because he is one of the 7 best quarterbacks on Earth.