The 396 is not really a true derivative of the W series engines. Yes, they shame the same basic bore spacing, and the same main bearing spacing. The rocker arms and the valve sizes in the high performance engines are the same. Only the rocker arms and rocker studs actually interchange, although you can use spacers to put a 409 crank in a 427 block (not to be confused with the W series Z-11 427 built in 1963) to destroke it.
And the "mystery motor" is yet another piece, it does not share that much with either the W series or the "rat motor". Yes, a "mystery motor" (outlawed by NASCAR) looks like a "rat motor", but it is not.
However, the W series engines were derived from medium truck engines, namely the original 348. That's the source of the real weakness of the 409 engines, piston and wrist pin weight. Had it not been for those two pieces being insanely heavy, the 409 would have been able to run at an even higher RPM and made far more HP. It's amazing what the 409 did achieve considering it was designed to power 2 ton trucks, and be governed at 4500 RPM.
A 409 has no combustion chamber in the head, the chamber is in the piston, that makes the piston extremely heavy. It does however make the valves unshroud almost instantly when they come off of the seat, which creates massive flow capabilities. Had Chevrolet been able to create a hollow "dome" style forging, and a tool steel wrist pin, the RPM limit of the 409 would have exceeded 7500 instead of being 6500. There's an easy 50HP there, making my old 409-425 (which actually made near 500) a true 525+HP engine.
The 396 was really a "clean sheet of paper" compared to the W series, although it shares some minor similarity. With a canted valve wedge type cylinder head (the most advanced of its time in the US), a forged crank, forged rods, and forged pistons, it was a true race bred piece. The second year of production yielded the 427/425, which was easily as powerful with one 780 Holley as anything Ford could build with 2 600 Holleys.