There are a few possibilities. One is that the origin of the name is intentionally ambiguous, just as many elements of the main story are, to encourage discussion with no clear cut answer.
In the older SureAI mod Arktwend, there is lore that Arkt and Wend fought a major battle, and Arkt's body was locked away in the halls of Enderal. The empire that rose afterwards was named Arktwend, combining the names of the faction leaders. So perhaps likewise the name of Ark was derived from Arkt because he was imprisoned there (if there is not more than one Enderal in Vyn).
I'm not sure all of the Vyn mods are entirely consistent in the use of names. For example, both Arktwend & Enderal have a "Northwind" location although they are different places, but that is a fairly common type of term. Arktwend and Nehrim both have a mage Callisto who may or may not be the same person. Arktwend has a dwarf named Tommy who sails away, and in Nehrim it appears that his body can be found in a beached boat in Nehrim, although it is speculation if it is the same person.