I think we have some illogical reasoning going on here. First off, just because a person believes in the Ark of the Covenant, doesn't mean he must believe in the "Sankara Stones." That is a fallacy of logic based on the idea that if one thing in the Indiana Jones films "exists" (I use this word loosely), that all similar things in the Indiana Jones films "exist."
I'm sure it surprises no one that there was a Sankara and there are indeed Sivalingas (or Shiva Ringas, which seem similar...correct me if I am wrong). Based on some rather lazy research I just did, five seems to have some significance to Hindis, and if our world counts as one level of the universe, and the seven levels above our world and the seven levels below our world are taken combined, then there are indeed 3 levels to the Hindi universe.
However, it also seems that the "Sankara Stones," using that nomenclature, and the existance of only 5 of them, seems to me to be something concocted by the filmmakers. Naturally, this occurs with the Ark and the Grail as well, but not nearly to the degree that the artifact in Indiana Jones and the Temple of Doom is not very true to the religion of origin.