I've spent a bit of time looking into this also.
If the numerical sort hypothesis true, then Primordial Malice would always appear first, not last, as it always does.
Also, you give the example of a MayongMistmoore hit, but prior to Kunark, the AgentsofMistmoore hit was replaced with QueenCristanosThex -- in the exact same position, with everything else unchanged. Proof:
http://tinypic.com/view.php?pic=2lsuf9&s=6#.WrBMPujwY2z
http://www.silverblades-suitcase.com/eq/mm_aoe.jpg
The hits clearly don't come in alphabetical order either, so it makes sense that one might argue for a "hidden ID#" hypothesis. But then this would be defeated by the reverse orders of StormGuard and EmeraldWarriors in the CrushboneOrc table versus the InhabitantsOfFirionaVie table. Another counterexample would be the reverse order of the Corrupt/Regular Qeynos guards in the SteelWarriors table versus the CircleOfUnseenHands table.
It seems much more likely that these tables are just individualized according to a list that belongs to the parent faction, and that the lists were populated by the developers manually. Almost all factions list as their second entry the faction most strongly aligned or most diametrically opposed: e.g. KaranaBandits lists KaranaResidents second, KazonStormhammer lists StormGuard second, CorruptQeynosGuards lists GuardsOfQeynos second, etc.
I would, however, be interested in any evidence that can support a different theory that has not been debunked by the above evidence.