If the rural people took back the cities, then how can this be considered a genetic ethnogenesis? The genes were there, in the rural area. Perhaps Rome had many immigrants, but this in itself would say little about Italy as a whole.
I'm sure a lot of port cities would have had immigrants and immigrant remains in their cemeteries. What will future archaeologists say about the cemeteries of Marseilles, or Hamburg?
Most of the large cities of the Empire were probably similar to some degree. Look at London today, or NYC, or some cities in Germany or France. How would they look to future archaeologists?
With time, with human nature being what it is, would there have been some admixture with "locals", with the probably exception of the Jews? Yes, I'm sure there would have been.
The issue is, what happened to the people in the cities? Cities get destroyed in times of war, and pestilence, i.e. Justinian's Plague, take a greater toll in crowded cities. People die or flee.
Even before the worst of it, the actual sacking(s) of Rome and most major cities throughout the Empire, the depredations of the "Barbarians" were taking their toll on the Western Empire. Everything started shifting to the east, to the "New Rome", Constantinople, and thank God for it, because they were able to maintain the culture and learning for longer.
Those who still had connections in the East, from where they could continue their mercantile and "industrial" activities, undoubtedly left for greener pastures. The poor, as is always the case, are the ones who have to just wait to die.
I by no means mean to imply that the more heavily Iran Neo/CHG ancestry didn't remain in Central Italy. We had it in the Neolithic. I'm convinced it moved into Southern Italy in greater numbers in the Bronze Age, and particularly in the Iron Age with Greek colonization. That ancestry moved northwards. We have it already appearing in very early Latins in Ardea.
What I am talking about is this "tail" into the Levant with which the people at anthrogenica are so enamored. It disappeared. I think the authors should have considered the possibility that it disappeared because the migration from that area ceased, and those who carried it might either have been transients, or after a generation or two left for other regions, or, just were more impacted by the calamities which befell the Western Empire because they were congregated in the cities which were hit the hardest.