the symbol is actually derived from an even older symbol in the phantasy star series. Which can be seen on the sealed ruins door after the Vol Opt boss match in single mode.
Tohru Yoshida, a character and graphic designer for both Phantasy Star II and Phantasy Star IV (also the director of PSIV) had this to say about the symbol in a recent interview from April 2017 for the MEMIDRIVE Phanta! fan book.
https://mobile.twitter.com/memiest/status/907573981162565632
Yoshida: I personally call it the Algol Mark. In the backstory details, it is a traditional emblem that has been long existent in the Algol Systems. The one that Rune has is the closest to the original. The one Rika has is the arranged version. The emblem on Raja's head too is supposedly an original version. A Dezorian version. "The Three Planets and the One Large Light" is the image and that emblem also represents something important as well.
So, based on that, I believe it is safe to assume the three big circles represent Parma, Motavia and Dezoris. Then the circle in the center, who looks like it has a connection with those external circles, might be the Sun, pretty much like in the original symbol. (I know, I might be stating the obvious here).
Now, what is puzzling me is the presence of the photon blasts names. What are they doing here?
But if I think about it, the photon blast are only seen with the mags, which does not seem to be manufactured on Pioneer 2 (no merchant sell them to my knowledge) but rather found on Ragol. And if you add that you start finding them in the mines and then in the ruins of the spaceship (which I understood was basically Algol solar system taking out the trash into the space because Dark Falz was starting to feel like a nuisance.), I would say they come from Algol too (stating the obvious here, maybe? I frankly do not know, I am a few decades late on the whole reasoning about the lore).
Then, I guess the photon blasts are somehow a way of manipulating "photon energy", like six big "schools" of manipulating it, developed in Algol solar system. Not necessarily a way to, well, blast things away, but if this is indeed technology from Algol, I would not be surprise to hear the only way the hunters understood how to use it is to make it explode in peoples face. (I mean, this is basically what happened when humanity first understood there was a way to unleash energy by breaking atoms.)
So... I might be going a bit too much on the "Dark Souls' lore" way of reasoning here (mainly with the idea of the mags only found in the mines and ruins so it must come from Algol), but do that seem plausible to you?
Or better, does anyone have an explanation of what are the photon blasts and why they are on the symbol of what is essentially Dark Falz's seal ?
Oh, and while I am at it : yup, this is one neat-looking symbol alright.