What’s it a door to? What does your builders say? Why is the flashing pealed back? Are you referring to the filling the holes in the top of the bricks with grout? If you were going to do it you’d use mortar. And it won’t make any difference if the flashing is installed properly. Plenty of YouTube videos on installing flashing over brick that would give you some background.

The door is to a living space, the builder wants ro fill the cavity with grout, however I’m concerned about moisture transfer between brick to inside slab. Due to the outside 2 brick heights drop, the weep holes where not installed as it would allow water in after the external patio to these doors was installed. The plastic you see is the termite barrier that folds over the bricks and sits under the doors.

Paint the slab with waterproofing??