How I think PSU is probably linked with PSO
PSO episode 3 timeline
http://www.espiokaos.com/misc/ep3_timeline.html
"Communication is received (on Coral) from another planetary search vessel of the successful discovery of another hospitable planet. Multiple immigration plans are discreetly put into action."
(My interpretation)
The inhabitable planet they discovered was actually the Gurhal Star System. That means that people in PSU are descendants from Pioneer 3.
"Han Walt begins the OPSS incident (a large-scale android massacre) believing it is necessary to control the population." "The androids who fled the massacre by escaping to the surface of Ragol report back to the Security Bureau."
(What I think happened next)
The information about the massacre reaches the Coral government (now immagrated to Gurhal) and starts a CAST civil rights movement that eventually triggers the 500 year war in Gurhal between Humans and CASTs.
Sometime during the 500 year war the communication between Coral and Ragol is lost and never is reestablished.
Also During the 500 year war records of history before immigration are lost and eventually forgotten.
At the end of the 500 year war the Tripartite Alliance Treaty is signed and the date system is changed from A.U.W. to BA (Before Alliance) and AC (Allied Century)
Now for what I think the SEED are.
In the Japanese version of Phantasy Star IV it says:
Several Hundred Million Years Ago - In an unspecified solar system, a civilization of spirit-life forms divides, and an interplanetary war breaks out.
2,000,000 Years Ago - The war is settled. As a result of the victorious side sealing the defeated side away, one fixed star and four planets are created, "Protectors of the Seal" are made on the four planets, and one kind of sentient life form is allocated to each.
300,000 Years Ago - The entire race of victors was wiped out. Except on the fourth planet, Ryucross, the beings of the other three planets, with the passing of each successive generation, begin to forget the mission of those made Protectors. Meanwhile, in their inter-dimensional prison, the sealed-away spirit-life forms transform into a wicked being, the accumulation of spirits of hatred and vengeance, and, at its core, a profound darkness is formed.
I believe that is a symbolic way of explaining this:
Before the confinement war the Great Light civilization had settled in two star systems, Algol and Gurhal. The civilization in Gurhal had discovered planet Ragol and had sent an investigation team to study the planet. On Ragol the investigation team ran into the subterranean creatures Saint Million, Shambertin and Kondreiu. The creatures infected the team with a virus (SEED Virus). The infected research team returned to Gurhal and the virus spread then had an outbreak. The first confinement war had begun. The Great Light invented the confinement system to get rid of the SEED. The confinement system in Gurhal was never fully activated and the SEED took over the civilization. The SEED then turned toward Algol, but Algol was ready. The Great Light civilization in Algol had been communicationg with the civilization in Gurhal. They knew the SEED's tactics. When the seed Army arrived in Algol there was a huge battle, many of the Great Light died. There was only a few Great Light left when they successfuly confined the SEED in Algol's "Dimensional Prison". While inside the dimensional prison the SEED combined into a single lifeform, the Profound Darkness.
The SEED in PSU are just SEED that remained in Gurhal and were never sealed.
In PSO episode 4, Saint Million, Shambertin, and Kondreiu are never explained as creatures that came from the Ruins, Altered Beasts, or escaped experiments. It also doesn't say that they came from the meteor that hits Ragol. They were just there. This theory actually gives them a purpose other than them just being a random final boss.
Dr. Osto's experiment, "Beta 772" was created by accelerating the growth of "D cells", the cells that carry the virus. His experiment became De Rol Le, a larval form of Saint Million, Shambertin, and Kondreiu.
"Dark Planet Ryucross" in PSU AOtI is where the last surviving SEED from the last confinement war made their base.
The Ryucross in classic PS is where the last remaining members of the Great Light reside. It could be considered "Light planet Ryucross".
After all "Ryuka" in palmalatin means "to return" and "cross" could refer to an X marker on a map, as in a designated meeting point. So "Ryucross" could mean something like "place to return to" sort of like a fall back point. possibly a safe zone to avoid containment when a dimentional seal is activated.