How will the inheritance be distributed after the father's death, and does the apartment I built with my own money enter into the inheritance? And should the father register the apartment in my name and my brother's name to safeguard rights, taking into consideration the sister's suggestion to make the ground floor an endowment for the daughters?

So, the father's permission to his son to build on the roof of his house is considered a gift or a loan, depending on the father's wording or the prevailing custom. If the father gifted the roof of the house to his son, then the building becomes the property of the son and does not enter into the inheritance. However, if he only gave him permission, then it is a loan (عارية) that ends with the father's death, and the building becomes the property of the heirs, and the son receives the value of what he built, dismantled. What the sister proposed constricts the daughters and deprives them of their right to inheritance or ownership.