If one looks at the prayer carefully, you will find that the intention is to pray from the particular to the general. The faithful are united in the faith by the visible head of their diocese. This is why he is mentioned in the prayer of the place where it is celebrated. The bishops are united with each other in the episcopacy (which is how we are united in the faith universally) with Peter at their head. This is why the pope is mentioned in the prayer. The Eucharist being celebrated is for those who have died in Christ, all the faithful, the clergy, united in the Bishop who is unitied with the episcopal college and the Bishop of Rome. When a diocesan seat is empty, the naming of the bishop will disappear (sometimes, if there are auxilairy bishops in a dioscese, they will get mentioned). The diocese of Rome is no different. Nor is it for the Masses celebrated around the world when that see is vacant. The naming should simply drop until a new pope is seated.
Now, that said, I can see where someone like the Dean of Cardinals (Ratzinger) could legitimately make an intervention such as he did. Afterall, a bishop will mention “me, your unworthy servant”, and so it might be appropriate for a member of the clergy of Rome (which is what a cardinal is) who is a bishop to mention the “episcopal college” or something along that line, in praying for his breathren in the abcence of the pope. Afterall, there is an intention following mention of the pope and the bishop of the place (in case of the pope, the same person) for the clergy.