This really only applies to those that already have their Atma weapon.

Basically what would happen is after you have completed at least one Atma weapon when you go back to the NPC he will hand you the 12 Atma crystals only they will be depleted. You then have to go back into each of the zones and do fates to recharge the Atma Crystal. After clearing each FATE with either a Zenith or Above weapon the crystal for that zone will receive a small amount of charge depending on the difficulty of the FATE. And yes these uncharged Atam crystals and the charged form would be in the key Items bag.

While this would not make the initial grind easier it would allow for people that like to collect the weapons to progress at more of a steady rate.