In short, the ḥadith is weak, and the heart finds no reassurance in its authenticity. Yet, if it were deemed sound, the answer would be as follows:
Second: The ḥadith does not say that the graves in question are visible inside Masjid al-Khayf. Al-Azraqī, in his Tārīkh Makkah (406-410), devoted several chapters to describing Masjid al-Khayf, yet never mentioned any protruding graves there. It is well known that the Sacred Law bases its rulings on what is outwardly apparent. Since no visible graves exist in that mosque, there is absolutely no objection to praying in it. The graves are leveled and unknown to anyone; indeed, were it not for this report—whose weakness you have already seen—no one would ever have imagined that seventy graves lie beneath its soil. Consequently, none of the corrupt practices that usually occur in mosques built over exposed or raised graves can take place there.
Reply to the Fourth Misconception
As for what is mentioned in some books—that the grave of Ishmael, peace be upon him,