I think that the Benefactor has their own agenda, and, as part of it, has ensured no comms to the MW or between arks/Nexus, as well as a lot of the mayhem of arrival. I don't know if taking down the sensors as well was intended, accidental, unrelated, or intentionally done by someone else
Just a thought, but if the Benefactor/someone had people up and monitoring the QEC comms, especially the one connected to the Geth super telescope, they could have gotten a good idea of what was going on behind them and what was going on ahead of them, and changed the game, either sabotaging the QECs or stealing them and replacing them with dummy boxes, plus setting it up so they could take off with what they needed for a solo colony or secret bases, and possibly take out "problem children" among the Initiative, including some or all of #1-7?
Also, how do we know it ACTUALLY took 600 years vs 650-700 as the ships play dead to avoid Reapers, etc. and someone on the ship fixed the clocks/destroyed the sensors/comms and evidence of what happened to those we left behind?
Plus, what if, a la Fallout vaults, experiments were being done on people during the trip. We know that the Krogan were being modified, and that the ex-Cerberus idiots were messing with people in Andromeda, what if there were other things going on, IE, what if the infected aunt running around Helios wasn't infected BEFORE the arks left, etc.?
Finally, what if there are more than just the Benefactor working behind the scenes on the Initiative? For instance, unless TIM was dumping all of his problem children on Andromeda, someone was probably doing it to cause him problems. Plus, there just seems to be so many conflicts/contradictions in the Initiative that there seems no way it is all controlled by one organized individual/group
