Now then... As for the nature of the Genesis Simulation.
For purposes of what I'm about to say, assume my theory about the history is correct in that the Federation was forced off/left Earth and went to space.
The URE stayed on Earth and used Tek. We know this because the obelisks have the jagged look to it, and the obelisks and were used to create the arks which were made after the war. The Federation developed Lunatek separate the URE's Tek, although the Federation was able to steal lots of Tek from the URE, as Santiago was noted to have managed to hack into a URE system and reverse engineer a Tek suit. There's no evidence about the URE having any similar ability to get Lunatek from the Federation, which is why there's a lot of Lunatek that we have no access to on Earth of in the Arks. There's no reason to assume that either side won a traditional victory. The moon blew up, but the Federation could've been on countless other places as well. And we know that the war on Earth was bad enough to create the Corruption that we had to destroy, so both sides were suffering from some extreme loses. It's possible they both decided that the war was too much and both backed out and decided on a treaty.
Since there's a split in Eletek, we can assume that it could easily develop to the point where Tek and Lunatek systems can no longer properly connect to eachother because they've became to different. Sharing information between Tek and Lunatek would then require a middleman in the physical world that could understand the working of both Tek and Lunatek.
Therefore, any Homo Deus that exists in the world of Tek, would be unable to go to the world of Lunatek; at least, not without something to serve as a connector.
This explains why Helena can't exist in our world or the GenSim for long - The Genesis Simulation is Lunatek and Helena is Tek.
This further means that Arat Prime which we know is connected to the Genesis Simulation, must therefore also be Lunatek.
Helena was able to access the GenSim for a short amount of time through Arat Prime, which would mean that Arat Prime is the connector between Tek and Lunatek, capable of reading both systems, but for some reason or another, maintaining a connection between Tek and Lunatek for a prolonged period of time, causing Helena to be unable to stay in the GenSim for long.
Further, this would mean that HLN-A is both Lunatek and Tek (which I will from now on refer to as Luna-Tek,) being able to both exist in the GenSim and able to read the Tek database to recover the answers to all the questions Helena asked so long ago in the genetic strand message.
Now, why does Arat Prime exist then? Wherever it is, it has Luna-Tek equipment since it's able to imperfectly connect Tek and Lunatek. The URE was busy trying to fight off the Corruption, and could not reasonably decipher Lunatek that they had no access to now that the war is over, so there is no way that Arat Prime was created by the URE alone. The Federation on the other, hand, had Santiago who was able to decipher the Tek systems at some time in the past, although it's entirely possible and likely that at this point no one could decipher the other side's Eletek systems. Either way, the URE has no chance of creating Arat Prime without help, therefore the Federation must've decided to help the URE after seeing the Corruption. If the Federation is offering to help the URE, there's no reason to believe they didn't cooperate, and we can assume that they did since magmasaurs were tested on Scorched Earth before going into the Genesis Simulation.
The best conclusion that can be drawn here is that the Federation, upon seeing what happened to Earth and having a common enemy, the Corruption, with the URE, decided to help the URE and create the Genesis Simulation, which could be accessed via Arat Prime, a location on Earth constructed by both sides with the purpose of getting the remaining citizens of Earth into the Genesis Simulation, and is capable of, to a moderate extent, connecting Tek and Lunatek systems
Further supporting this idea, the GenSim is supposed to be a method of escape.
Arat Prime going on lockdown means that anyone still on Earth is abandoned. HLN-A tells us that there are 0 humans still on Earth (meaning Diana and Mei must've left to the GenSim or off-planet as well,) so everyone had either reached Arat Prime or was about to die by this point.
'Launch unconfirmed' now becomes much more problematic than originally assumed. If Arat Prime wasn't properly able to get people off-planet or into the Genesis Simulation (unable to launch,) then that means that everyone on Earth died. The entire URE. Every single person. This is, unfortunately, the more likely scenario, since Diana and Mei had to go to Arat Prime for Helena to use it to get to the GenSim, implying that things weren't right there.
Now, here's where things really start to get going.
Rockwell, as we know, has his own element strain, different from Corruption, Tek, and Lunatek. Since he connected to Aberration, he created a connection from his own strain of corruption to Tek; however, thanks to the original homo deus, Rockwell is unable to exercise the power in the Tek system that he'd have without the deus stopping him. Naturally, the deus are Rockwell's next targets in his quest for godhood. Since Rockwell has access to both a physical body and Tek systems, he theoretically should be able to become much stronger than a deus, which is purely in Tek, and will therefore eventually overcome this obstacle if left unchecked. Helena must therefore have decided either one of two things:
1) Rockwell taking over the Tek systems is inevitable, and the only way to stop him is to gain access to Lunatek before he can take over the Tek systems and beat him afterwards.
2) The only way to stop Rockwell in time is with Lunatek, so survivors must go to the GenSim as a step to getting Lunatek to be able to stop Rockwell
Either way, Helena has decided that Tek isn't enough to stop Rockwell at this point. This might be because Tek stopped developing with the death of the URE, while the Federation is separated from the Corruption and still alive out in space, so they're able to still progress (assuming they didn't meet their own fate that we don't know about)