This manuscript develops Binary Layer Theory II as a projection–aggregation framework for prime-pair absorption across binary layers. Building on the binary closure coordinate introduced in BLT-I, it studies how a binary layer partitioned into B source bins expands into a B^2 pair-space and is projected back onto B target channels through diagonal aggregation bands. The paper establishes the Binary Projection–Aggregation Geometry Theorem and the Balanced Even-Depth Stabilization Scale Theorem, showing that the natural stabilization scale induced by binary projection–aggregation is the square-root closure scale sqrt(2-S_K).