The article you cite to doesn't say the bones of St. Peter were never in Rome. It says that the Francsicans currently have them in Jerusalem.....or that they're in England somewhere as of approximately 600 AD. I dunno.
Is that what you want us shameless mackeral snappers to say?
I believe that it says that the Franciscans discovered them in 1953 beneath their monastery there on the Mount of Olives, not just that they have possession of them.
And just recently the Vatican says that it discovered the bones of St Paul beneath the cathedral of St Paul there in Rome. So just whose bones were shipped to Britain in 665 AD is anybody's guess.