The Magnus feat doesn't contradict this. Dublicate 616 ist still 616, an dublicate.
Galactus might be so much more powerful then Mephisto to beat him like the spectre, but you know what the analogy was meant for. There are beings who are supreme in their own realm, even to more powerful beings, it's nothing special. 😉
Erasing an timeline is an universal feat, sure, but this is the power of the time gem, the power over time. You control one aspect of an universe, like space or time, what's so wrong that you can destroy said universe by eliminating this part. There can't be an universe without time, there can't be an universe without space.
Each gem is universal fot it's universe, but that doesn't mean that all gems together are more then universal.
IIRC JLA/Avengers correctly. Darkseid seized the IG but even though Desaad confirmed that it is omnipotent, it was useless in Darkseids reality. I know, it's non-canon on this boards, but still it makes more sense.