Interesting, but suppose parts of bones could be found in other locations? It is not uncommon for Saints to have the major parts of the skeleton in one place and pieces of other bones elsewhere. I suppose that it certainly could be possible. A good example of this would be St. Philomena, who's skeleton is housed in a statue in Italy but also has other bones and fragments in reliquaries around the world. We even have a reliquary with what I think is a piece of bone here in Houston. It's at Queen of Angels (SSPX) in Dickenson, which the church used to be famouse for.
(From memory.)
I think the skull is NOT with the bones beneath St. Peter's Basilica and this was not a surprise when they were discovered, as the skull of St. Peter is preserved elsewhere. (If I remember correctly.) I read about this years ago and the archaeology behind it is sound. St. Peter was buried in a small grave next to a wall in the cemetery on the Vatican Hill. If you crossed the Tiber and headed up the hill on the road, or street that was there, to your left would have been an amphitheater which Caligula had built, and to your right was a cemetery, and farther up the Hill were gardens owned by the Imperial family. St. Peter was crucified in that amphitheater. Christians were burned to death like living torches in those gardens.
When Constantine built his basilica, he had a large part of the hill excavated (I think he carried three baskets of dirt in the operation himself) and that cemetery was buried. The one wall of the amphitheater became one of the foundations for the new basilica, its "left" side,as it were. The altar was built over where St. Peter was buried. They had a steps going down to the site.
When they built the new basilica in the 1500s, they did not make the grave accessible any longer. The steps under the altar went down to a chapel over the site, but you couldn't get to it anymore.
What happened in the 30s was there was an excavation beneath the basilica and they excavated the old cemetery. When they got to the spot beneath the altar, they found the old wall. There were no bones in the grave except animal bones. (not uncommon.) There was a niche in the wall in which they found the skeleton, without the skull. ther was an inscription in the general area also that read "Peter is here." After studying the bones, they concluded it was St. Peter.
The skull was missing because at some point it was deliberately taken to another church (I forget which one) in the days of the first basilica.
As to why the bones were in the wall, this is the theory: During a Saracen invasion of the city (900s?) the bones of BOTH Peter and Paul (and perhaps others) were taken OUT of their graves and hidden somewhere for safe keeping. After the crisis, they were RETURNED. The theory is that at this time they put Peter in the wall. That may or may not be correct. We know from the work done just the other year that Paul was put back in his place. Like Peter, his tomb was later made inaccessible (that was probably in the 1800s when St. Paul's burned down and had to be rebuilt.)
So, having said all that, I would guess that these are some relics of the early popes that were put in this church sometime between the 300s and the construction of the current basilica.