What is the purpose of baking a cooked pot pie filling?
Good pot pie has a layer between the biscuit or pie crust and the filling. That layer is goopy, it takes on properties of both of the other elements. Without that kind of middle layer, the two elements would be missing that unifying texture. That said, it's not a big deal. Just be sure that the ingredients in the filling are truly optimally cooked.

If the fresh biscuits can live on the filling for even a little while, that will help that texture issue.