Semi-correct. The end of ep 6actually reveals that the Photoners did not create the Profound Darkness.
The following is spoilers...
The Profound Darkness is the dark part of your character, who is the primordial being. All beings have a dark side, yours just happens to be the PD which exists at the beginning of time. From the Time Line's point of view you pop into existence along with the PD and as time pass with nothing happening the PD diminishes as there is nothing to desire to destroy and although the light diminishes as well, hope, the light, exists still as does your mind with all its knowledge. This results in the light, you, becoming the akashic record while the PD is just a small flicker kept alive within you but also separated from you as that flicker.
When the Photoners find Shion, who is a sentient planet able to access and commune with the Akashic Records... that is, you, they attempt to clone her. That is to say, they attempt to create another conduit to the akashic records and to themselves, but these all fail or have some down side to them. Their AIs or connection or form isn't right. The First one created, while near perfect, is still flawed and thrown into sub-space, eventually emerging into a new universe and becoming the Moon and Mother. Later iterations have AI issues, 2 of which have opposing issues and it is attempted to merge them together resulting in the planet Amduskia. The final attempt works almost perfectly.
The Final attempt connects the Photoners with the Profound Darkness portion of the Akashic Records, you, the Light, The primordial being and with it comes the enhancement will and emotions, particularly negative ones which turns regular photons into F-Factor (I forget if it is D or F, so I'll just go with F) or anti-photons. It also causes several regular photoners with particularly negative emotions to spiral out of control and become Dark Falz. In an attempt to fix this problem, ARKS is created as is research into vessels that can absorb and house anti-photons as a means of combatting the F-Factor. This results in a new sentient being to be created, Harriette, who's soul (which is not Photons) is then ripped from the vessel and then it is used to absorb "all" of the F-Factor, which is the dark side of yourself, separating the light, The Akashic Records, from the Dark, The Profound Darkness, and creating Shiva... who is then tossed into sub-space.
At this point the ARKS fight the Falz that have already been created and it is impossible (probably) for another Falz to be created. They are all Photoners who transfer from body, corrupting them and the creatures around them. The reason that ARKS is not able to succeed in defeating them is likely largely due to the fact that Elder, Apprentice, and Gemini all have their negative emotion catalyzed by things that would cause them not to fade over time, although I doubt the thought was put into this and it just happens to be a coincidence, but the idea with the PD and F-Factor is that they actually weaken over time due to acceptance or some such element which satisfies the thing that they are craving. The PD's craving is destruction of all (kinda scary that Sega is saying that you have that neg emotion, but whatever) and when there is nothing the PD slowly dies. However, Elder's thing is challenge, Apprentice is loneliness/Outcasted, and Gemini's is fun... All three of these when you put them in a seal causes them to strengthen or maintain for the most part which if there were more Falz it explains why we see only these 3 and why they're such a pain to get rid of.
If you're going to take issue with me saying no more Falz can be made... Luther becomes Falz only when connected to the Akashic Record, Persona is created because you are the akashic record, and Matoi's PD can be explained as she is another clone of Shion of some sort thus is connected to the Akshic Record.
New Genesis happens because you interacted with Earth. This is the only timeline where You did that as the story says that you have become entangled in the fate of multiple universes. Omega doesn't count, but removing it still leaves Earth. By interacting with both Earth and PSO2-verse the story implies that the cosmos will not let a particular timeline just disappear and thus gives the ability to "You" to separate from the Akashic Records and the Profound Darkness and because that is how that works the PD and Akashic Record are sealed away in that time loop while the rest of the universe which would have ceased to exist had this not happened is allowed to continue on... But here's the thing... The Akashic Record still stands because photons still exist and they are the recording instrument of the universe, but we also know that this stuff exists outside the universe so time is wonky. The Akashic Record will always remain outside the current universe and as a result some element of the PD will also exist because they are one in the same.
Also... remember that the creation of Falz and the PD is not something that is inevitable, but rather it is the fact that being able to manipulate photons on a high level PLUS having negative emotions can cause anyone to lose control and eventually become a Falz while PD requires a connection to the Akashic Records that will eventually lead to a will to destroy everything.
The thousand year thing is likely the result of negative emotion build up ^.^ or that is how long they surmise it takes to create the tech to construct a way to interaction with the Akashic Records... or just for a Falz to get strong enough to bust through a seal or for someone that powerful and dumb to come into existence. I dunno, that part is never really answered in any way. It's a convenient number that allows you to mess around a bit.
k k done rambling.