What is the wisdom behind including the tomb of the Prophet, peace and blessings be upon him, and some of his companions within the Prophet's Mosque, knowing that it is not permissible to bury the dead in a mosque and that prayer is not allowed in any mosque that contains a tomb?

Several hadiths have been narrated from the Prophet, peace and blessings be upon him, prohibiting taking graves as mosques, and from plastering and building upon them, due to the potential for shirk (polytheism) and the worship of their occupants besides Allah. The Prophet, peace and blessings be upon him, and his two companions were buried in Aishah's house, not in the mosque. The chamber was only incorporated into the mosque for expansion, and this does not serve as proof for the permissibility of building upon graves or taking them as mosques.