Dunno about that. In TOS, all the really bad baddies were from outside the Milky Way: the Doomsday Machine, the Kelvans, the Flying Pancakes...
What they had in common was an utterly un-humanlike physiology. One is almost tempted to think that each galaxy at this day and age is under the control of a single superspecies that only allows its own kind to flourish there, and the Milky Way has humanoid overlords (that is, they used to be humanoid and are still fond of that shape) while Andromeda is controlled by somebody who used to look more or less Kelvan (that is, with a hundred tentacles).
Being extradimensional confuses the issue of being extragalactic. The Organians weren't of this world, but they did seem awfully jealous about Organia the planet. Are the machine intellects perhaps chauvinist about specific realspace locations, too?
Well, as said, they voluntarily went away when the Advanced Synths stopped ringing the welcome chime.
Looks like politeness or shyness, and I don't think it would be logical to associate shyness with the great power suggested and, to a degree, demonstrated.
Being polite doesn't necessarily mean being benign, though. Perhaps they will politely wipe out all organic life, or discreetly force it to meld with machinery, or courteously usher it into ghettoes so that machine life gets room to expand.
This specific instance is an odd one to interfere with worldly affairs. Why would the super-AI community care about the Advanced Synths more than they do about the other sorts of Milky Way AI in Star Trek? Why won't they intervene for their brethren when Kirk is killing them, or when Janeway is?
Timo Saloniemi