For Joseph's Tomb in Nablus, the usual claim is that it is really named after location of a local sheikh/miracle worker, Yusef al-Dawiqat, who died in the 18th century and was coincidentally also named the Arabic equivalent of Joseph.
Which is why I found this story in a Palestinian news site surprising:
500 settlers storm the tomb of the Prophet Joseph in NablusHundreds of Israeli settlers stormed Joseph's Tomb in Nablus at dawn on Thursday, under the pretext of performing their prayers, under heavy security guard from the Israeli occupation authorities.
No scare quotes around "Joseph's Tomb," no reference to Dawiqat. It appears that the news site accepts this as legitimately Joseph's tomb.
However, this is an old story, from 2013. \\
More recent stories in Palestinian media about Jews visiting the site make sure to add that they don't believe that it is really Joseph's tomb, indicated by not saying "Prophet Joseph."
If it is the real resting place of the biblical Joseph (which is far from clear,) then Palestinians have no reason to ban Jews from visiting. So it is easier to rewrite history than to allow Jews to do pilgrimages in an Arab majority town.
