Word Origins : Places and Objects
Absorption Gate
Just as its English name implies, "Absorption", the gate which absorbs the Cell Particles given off by the Radiation Gate.
The 5th Qliphora, Akzeriuth. Translated as cruelty.
It was said to base off the land that is rumoured of wealth called El Dorado, back when Spain was having its great expeditions.
The 1st Qliphora, Baticul. Translated as Atheism.
The research facility is probably based off the one who invented telephone, Graham Bell. In Japanese it spells "Beru-ken", to which the word "ken" is short for research facility in Japanese. Or maybe it's based off the 8th Qliphora, Gemdah which is translated as Greed.
Capacity Cores
Some C. Cores, such as Tutti, come from musical terms.
The 4th Sephira, Hesed. Translated as mercy (benevolence) or the love of God.
The hidden Sephira, Daat. Translated as knowledge. This Sephira is different than other Sephirot because it is said to be found on top of the depths of Sephirot - the Abyss. In the story, Daath is a part of the monitoring program of Yulia City.
It is believed that this is based off the 5th Sephira, Gevura. Geruva means strict, rigorous or stern.
Feres Island
Probably based off the 6th Sephira, Tifaret. Speaking of which, it was translated that Tifaret mans beauty.
Grand Chokmah
The 2nd Sephira, Hokhma. Translated as knowledge or intelligence. It also means the Highest Father.
The 8th Sephira, Hod. Translated as Glory.
The 6th Qliphora, Kaitzul. Translated as abominable.
The 1st Sephira, Keter. Translated as crown, thinking and creativity, and the closest to God. "Berg" means a mountain on its own (without other mountain ranges nearby), and "burg" means city/village.
It is believed that this is based off the 10th Qliphora, Kimlanud. Translated as Materialism.
The 10th Sephira, Malkhut. It is translated as Kingdom, the material world in which people perceives.
Nam Cobanda Isle (Namco Isle)
In the Japanese version, it's just a parody off the original maker, "Namco". In the English version, it points to "Namco Bandai".
Nebilim's Crag
In the Book of Enochi, Nephilim refers to people created by the crossbreeding of God's sons and the daughters of man. It was said that the Angel, Gregory, who God sent to monitor humans was tempted by a daughter of man and fell from the heavens. Other than being crossbreads, Nephilim can also be loosely translated as Titans/Giants.
Ortion Cavern
It is not known whether if Dist's middle name came from this cavern or it's a comic ironic reference to which Dist himself winds up working in the Ortion Cavern to complete his theory on Fomicry.

[Note: In the Japanese version, Ortion Cavern is called "Wyon Mirror Cavern" and Dist's real fullname in Japanese is "Saphil Wyon Nath" and his fullname in English is "Dist Ortion Neis". For more info, read Dist]
A tree that has the opposite symbolism of Sephiroth. It also has other meanings like empty shell and outer shell. It is called Qliphora in its singular form. Every Qliphora corresponds to every Sephira with a immorality. In the Japanese version, Qliphorth is refered to as "Makai" in written Kanji, to which the English meaning is "The Realm of Immorality" or "Hell".
Radiation Gate
Just as its English name implies, "Radiation", the gate which proliferates Cell Particles.
A score is another word for sheet music
It came from the tree which was planted in the Garden of Eden in the Old Testament. In Kabbalah it symbolizes the universe. It is called Sephira in its singular form. There are 10 Sephirots which are connected by 22 paths, and each Sephira corresponds to a virtue.
It is believed that this is based off the 3rd Qliphora, Sheridah. Translated as rejection or denial.
Shurrey Hill
It is believed that this is based off the path between the Hod Sephira and the Yesod Sephira.
St. Binah
The 3rd Sephira, Bina. It is translated as understanding (verstehen). In contrary to Hokhma, it means the Highest Mother.
It is the name of the underworld (even lower than Hades) and a deity in the Greek Mythology. Highlight for spoiler: [In the game, the Tartarus was casted into the core (which in a sense is deeper than than just an "underworld").]
Tower of Rem
In Abyss, it is the tower which contains the collective conscious of the 6th Fonim with the alignment of Light, Rem. (Basically the Tower of Light if you will.) The word Rem is probably based off the unit that refers to the absorption rate of the radiation particles from organisms.