Is Atomos trying to help us?

[Inaaca]

or the crystals come from the aetherits that atomos drained to make stronger monsters .

I seriously doubt Atomos drained the Aetherites. If that were the case, we wouldn't be able to teleport there at all anymore. They would be dead crystals.

Instead, we can teleport there cost-free and they're a new golden color. If anything, I would say he supercharged (over aspected?) the Aetherites, making them even stronger.