Layers aren't really a thing. What are a thing are particles on top of one another instead. The only thing that really matters is which one is on top, because that's the one its neighbours will see, and this is always the particle with the highest ID among the ones in the "stack".

LCRY has four states: inactive, activating, active, deactivating. The LCRY under the PSCN starts from inactive and never gets activated because SPRK never sees it (under itself). It does see the adjacent LCRYs though, and that it transfers to the activating state. When these LCRYs finish activating, they transfer to the active state. LCRY deactivation is done by inactive LCRY looking for active LCRY to transfer to the deactivating state, so once the visible LCRYs become active, they are immediately transferred to the deactivating state by the LCRY under the PSCN, which is inactive.