There’s a canon manga called Lunar: Vheen Hikuusen Monogatari (???), which gives a lot of additional back story on Ghaleon and the other heroes of Althena. That’s probably the other problem behind the unanswered questions of Lunar… although Working Designs can’t be faulted for that. The manga and various art fanbooks explained stuff, that players in Japan would ask, therefore closing loopholes. There was another canon manga called Lunar: Yonenki no Owari, which covers what happened to Phacia and Xenobia. It takes place during the time frame Lucia left Hiro, and he was hunting for a way to the Blue Star. Finally there’s a canon Lunar 2 manga that retells certain points of the game’s story in greater detail and sometimes from Lucia’s point of view.
All are canon because Shigema Kei gave input and blessed them so (who is the creator of Lunar). Lots of interesting points are revealed in them. For example 3 years had passed before Hiro rejoined Lucia, after Zophar’s defeat. Ronfar and Mauri have a little girl during that window. Jean and Lemina - much to their horror - are still single.
As for the game itself… another major item omitted by WD: there’s some strong hints that Lucia and Althena aren’t goddesses per se… Lucia makes reference that her purpose is safeguard the Blue Star, and that she exists only for that purpose, which is why she had to leave Hiro despite her wishes. It’s also the reason why she was willing to obliterate the Silver Star if it wasn’t for her devotion to Hiro (Althena was guardian of the Silver Star; so Lucia wasn’t bound to protect it). Some additional hints here and there, seem to indicate that the two were created for their purposes. Putting two and two together, the pair may represent what humans USED to be like. Sadly Zophar’s origin was never really explained (in-game or manga extras), although is intimate knowledge of Lucia and Althena, indicates he predates them. Maybe he was their prototype that lead to humanity’s original fall. The whole artificial creation thing, also explains why Althena and Lucia were originally emotional blanks. If they created humans in their image, the sisters shouldn’t have been so ignorant about them, or themselves when interacting with humans.
Another item to note in the epilogue of Lunar 2: notice how the various Shrine Guardians back to the Blue Star, have a decidedly mechanical look to them. Not to mention the whole “fallen advanced civilization” imagery, which is all human-centric (beastmen and demons, even at their respective heights, had nothing like it).
While it sucks hardcore (although mostly for tremendous gameplay redesign), Lunar: Dragon Song was also written by Shigema Kei. From this entry, we learn humans arrived on the Silver Star as primitives. However until they arrived, there was no Althena or Four Dragons. We also learn Althena isn’t the most faithful woman in the cosmos: seems like she’s screwed every Dragon Master there’s been. :o
Lucia evidently ages if she’s not in that crystal stasis - another unexplained reason why she had to leave Hiro. Ultimately I suppose Hiro and Lucia are hibernating in that crystal together. We’re really not given an indication of how much time had passed between the moment Hiro awoke Lucia after reaching the Blue Star, and the credit scene when the pair see grass growing. Hiro shouldn’t complain though: not a bad way to spend eternity, naked and cramped together with Lucia.