I just want to clarify something I wrote in the Scavi post. As I recall, the tour guide (who of course was not just doing her own thing, but was acting as a representative of the site managers, aka the Vatican) was carefully-almost-agnostic about the bones. She didn’t quite say "We don’t know" but she did say, "It’s interesting that they didn’t find feet…it fits in with the stories of Peter’s martyrdom" and she did say "They could be" and "If they are…"
So it seems to me that even though the remains are carefully preserved there, the emphasis is not "Here are St. Peter’s bones." Rather, the emphasis is: the archaeological excavations have revealed that this is the spot where Constantine built his altar on top of the spot that had been revered for centuries as Peter’s burial spot."
I think that’s an important distinction to make…and I came away from the tour hearing that distinction rather subtly, but truly made by the tour guide.