Fridge Brilliance: There's no Holy element in this game. Instead, there's "Sea" and "Curse". Sea is actually sacred in this game so it's the "Holy". This also means that water-oriented spells like Spread, Maelstrom, Tidal Wave, and Aqua Laser are basically light-elemental spells, and thus Brilliant Lance, Judgment, and Ray (traditionally light spells) are sea.
Fridge Logic: The hidden door at the Ruins of Frozen Light. Yes, Jay could have just told the party about it, but there was a closed door behind the hidden door. Either way, they would have had to go through the Great Hollow and the Underground Lake to get inside the Ruins, due to the second door that was behind the hidden door. Seeing as they opened the second door from inside the Ruins, they couldn't have gotten in even if Jay told them about the hidden door.
If the Ferines can live in the ocean, why bother living on land at all?
The sea had been extremely rough ever since the Orerines created the first landmasses. Presumably, it was too rough for the Ferines to live in.
How do the heck Orerines able to use eres? Since the Raging Nerifes is the source of that power and Orerines are the ones who brought trouble to the planet and 1. They are from a different planet 2. They are the ones who terraformed that planet and causing the seas to become abnormal and 3.Orerines are killing its servants/worshipers., why would Nerifes grant them the use of eres if they cause so much trouble for it and the planet? Was it a mistake? Did it hope that Orerines would wipes themselves out with the power? Are all the Orerines erens are somehow descendents of interbreeding between a Orerines and a Ferines? Why?
I believe it's mentioned somewhere that Eres only appeared among Orerines within the last fifty years. So there is definitely reason to believe the interbreeding theory. Though considering the state of relations between the two groups, that has its own uncomfortable implications.
An alternate theory is that the "Quiet Nerifes" granted the Oerines the power in hope that they would calm its rage.
Why are only Ferines able to fire the Legacy's weapons? It an Orerines ship. Presumably it had weapons even way before the Orerines had contact with the Ferines.
Fridge Horror: Chances are... the weapons were made after they landed... and adapted to use the Eres of the Ferines. The Ferines obviously decide that the end justifies the means.
The Nerifes Cannon and Wings of Light both use the Ferines as a power source, so it's likely they were either built or heavily modified after the Orerines landed on Shining Blue. Since the Ferines power the weapons, and the ship's systems had effectively been powered and controlled by a Ferines for three years prior to the start of the game, it makes sense that they can also use them.