The north is a frequently used theme in both CT and CC. In CT the Northern Ruins and the North Cape are places where good and evil seem to be ambiguous--both Magus and Cyrus seem to be both good and evil. The Sun Keep is on an island that is furthest north. and Zeal is as far north (and up) as one can go.
In CC the Porre Army and any mainlander come from the north to El Nido and cause all sorts of havoc. Norris' name even means northerner in celtic (I think celtic).
In Babylonian, Mithraic, Egyptian, and Christian traditions a common theme is that both the greatest evil as well as the greatest good both take their throne in the north. People even pray facing north in some traditions, all the while knowing that the greatest evil is said to exist there.
Also, the northern wind is frequently seen as evil. Since it numbs the body with cold, it is thought to numb the spirit with evil. The fact that Norris-- who's name means northener and who also comes from the north--is a member of the "black wind" lends further evidence to a connection. This could be a clue as to where the "black wind" has a real world reference, although I have only seen a few mentions of it in myth and dream analysies.
Anyone else who has noticed any other northern themes, feel free to jump in.
North, in Chrono Trigger, to my mind, is simply a direction. I don't see it as taking on any deeper meaning. The East is the abode of the Mystics; Guardia is sort of central. To the west is El Nido. North and South are never introduced, save for Porre which I suppose, if one stretches the imagination, is in the south.
To be honest, however, I cannot recall north being looked at as a stronghold in either Christian or Babylonian, or Egyptian myth/legends. I know very little about the cult of Mithras (save that he was a Persian god of light, and came to be a popular mystery religion amongst the Roman legions), so I will refrain from any comment there. Babylonia would have held itself at the centre of the universe, even as the Assyrians did, and the earlier Akkadian speaking people (of which, it might be said, the Babylonians were a part.) In the beginning there was Tiamat and Apsu, which encircle the world. Later, after Tiamat's defeat by Marduk, the earth is created, but I do not remember much reference to a north; most is either central looking or, if anything, I would think to the cities in which the great temples reside (Nippur, or Lagash... cities of that sort.) Overall, I think they were a touch too myopic to look anywhere else, especially to the north (and who were there? The Mittani? Not exactly a big threat.) As for Egyptian... here I will concede to knowing little. I cannot rightly remember the battles between Horus and Seth, so perhaps I'm forgetting if one or another takes refuge in the North. But Thebes, longtime capital of Egypt, was in upper Egypt... that's south, geographically speaking. Thus I would think their view to be to the South and, because of the sun, East and West. And as for the Christians... no great evil I can think of ever comes from the North. Indeed, in that sort of history, the greatest military foes can be seen as being those of the East, the Huns, and the South-East, the Turkish Muslims (ie. the Crusades.) I'm somewhat hard-pressed to think of where in the North there would have been a theme of taking up a throne in the north. By all accounts, from what I know of history and the tales of Arthur, the north of Britain would be an untamed and mysterious land, but the foes were Saxons, from the continent. The ones who would, actually, hold some idea of a northern throne would be the Norse. I'm not certain, but I think that, with their manifold Rime and Ice giants, more than one of those terrible creatures was thought to have a fortress in the frozen wastes. But to be honest, I'm not exactly sure what you mean.
In Chrono Trigger, the north, as I have said, is rarely spoken of. When it is, it is used simply as a name. Northern ruins, and that sort of thing, but not the North as 'fantasy' has come to know it. That tradition, if I'm not mistaken, is about eighty or so years old and begins with Tolkien. Most probably only know of Sauron and his kingdom of Mordor in the South East, but Sauron was hardly the greatest of Tolkien's foes. Far more terrible was the Dark Lord of the old North in the Elder days, the battles against which are the chief tales of his Silmarillion. That, and nowhere else more clearly, is the North seen as a menace. North lies Thangorodrim, the Mountains of Oppression. North lies Angband, the dread fortress that is synonomous with hell. North is Morgoth, the Dark Enemy, foe of gods and Elvish race. For four hundred years the Elves of the Noldorian kindred hold a great siege about that fastness, but theirs are battles doomed to failure. This is an idea, the chill north where resided an ancient lord of unfathomed power, that has been latched upon by many fantasy stories, I think. I would think that is where the idea of the great thrones of the north comes from, because it doesn't fit with any other myth I remember.
But to speak precisely to Chrono Trigger/Cross, and to reiterate, I cannot find anything that actually fits that theme of a strong and iron north.