Most magnets should respect setting a boolean tag named PreventRemoteMovement for the item entity to prevent them from being picked up.

Once turned into the real crystal, it should be removed.

The removal should be automatic, I think we do not inherit entity data when we remove the seed entity and replace it with a normal item entity.

In case of seeds the entity will be kept and only the itemstack is changed. For example it ensures that the finished crystals do not despawn.

Ah yes you are right.