Transform + Rage completely upsets the balance of the game, while the Pomeg Glitch does not. Illegal egg move combinations are simply impossible to get ingame without using a Transform + Rage glitch or similar.
Because the Pomeg glitch only affects Little Cup, and nothing else, if my memory serves correct. It only allows you to learn level up moves and gain EVs as an egg, which has no bearing on level 100 play at all. I don't think this makes level 1 Donphan legal, though, but that isn't entirely relevant either.
as one of the guys who helped make the decision, I agree it is kind of arbitrary. but, Pomeg presented an opportunity for several Pokemon to become viable when they hadn't previously, whereas rage+transform had the significant downside of completely destroying any semblance of balance not only in Our Faire Little Cup, but in all the tiers. wonderful as I am, I don't have the right to make a call like that, so that was never on the table. Nobody but LC gave a fuck about Pomeg, so it stuck around.