Regarding the Faro Plague and the various machines of the Chariot Line being frozen in mid attack while at least half a century would pass between the end of Enduring Victory and the Swarm being shut down by Minerva,
Given that in the Datapoints The Bad News General Herres says that “There will be no Earth left to reclaim. Just a lifeless, toxic rock with several million Faro robots on it...hibernating, waiting for something to eat.” that would indicate that in the absence of any detectable biomass to consume if the statement was taken literally then the Swarm would essentially remain immobile from their current position until they would detect any signs of biomass
And in the Datapoint Biosphere Degradation the timeline of extinction of “exposed human populations in February 2066, extinction of macrobiotic land organisms by the end of March 2066, and extinction of marine life in early 2068.” Would indicate that all available biomass available to the Swarm would have long been destroyed by the time of Minerva being able to deactivate the Swarm,
Though some of the machines in the Swarm would have been destroyed by the forces of Enduring Victory before their final collapse, explaining at least some of the Swarm’s numbers, given that EMPs were used against the Swarm it could explain at least some being frozen in mid attack, particularly in the Gravehorde/US Robot Command and the battlefield in No Man’s Land in the Forbidden West, there would be an equally if not greater amount of machines that would be somewhat unaccounted for, most notably the Metal Devil that was deactivated and dormant on top of All Mother Mountain
As the coincidence that the Swarm was deactivated by ZD just as the Metal Devil was about to attack the Cradle within the mountain would be somewhat to perfect last second timing, combined with the lack of any other Chariot line machines or Enduring Victory forces nearby either trying to attack or defend the Mountain and the Cradle within would be something of a disconnect in the lore, with the remains of the forces of Enduring Victory being present in the timeframe of the games
Though I think that GIAI leaving the remaining Chariot line machines intact even after they were deactivated would have been a mistake, particularly considering that the new generation of humans would be unaware of the threat that the Chariot line would face with the destruction of Apollo, with GIAI during her terraforming should have at least disassembled the Chariot line and recycle them into the machines she would use to rebuild the entire world, to ensure that in any scenario that the Faro Swarm would not be reactivated again under any circumstances
Though again according to The Bad News datapoint there were at least by the time of the creation of the hologram seemingly in the early days of ZD, there were at least 1000 Metal Devils in the Swarm, combined with the 15 months timeframe of ZD and the area around G Prime being the last point of defence against the Swarm, with their being 5 Metal Devils in the map area of HZD, and a combined 12 total in the area of the games,
I would almost expect a higher quantity of Metal Devils to be littered around the map, maybe having rows of fallen titans being on the shoreline of the western seaboard, given the description in various datapoints, though I can understand in terms of real world design that having the full coast being nothing but titans would be somewhat strenuous on the visual side, though a powerful background image, maybe the fallen titans could have been over the centuries been covered by the increased water levels
Also given that in the Datapoint Sobeck Journal, 10-31-65 R it is said that the Swarm went through straits of Magellan from Antarctica and that the Swarm came out of the ocean when attacking the west coast I would suspect given that ocean life was protected to be destroyed by 2068 and that there was more water than land on Earth that given that the Swarm follows biomass that the Swarm on land would only consist of the machines that were destroyed in battle, with the majority being under water given that the last biomass on Earth was located in the oceans, with the possibility that NEMESIS would seek to awaken the remaining machines of the Faro Plague to attack humanity