1) Atomos is from the Void. The closer Dalamud got, the more it messed up the Aetherial energy flow of Eorzea, like how the moon effects the tides. It made things unstable and creatures from the Void found it easier to come here. It seems to me he's just a creature that feeds off of Aetherial energy, so he goes to the places with the most of said energy, the Crystals. Nothing more involved than that.

2) After Louisoux dies (maybe), there are still 11 more Archons that could have tried other things. And obviously someone has to imprison Bahamut in the Labyrinth, he doesn't just go there willingly. It could have even been Gaius van Baelsar. We don't know, and they'll probably explain it in 2.0.