Mod vs Mod, yes a b16 will outperform a d-series engine. No contest there. BUT level the playing field, mod for mod, a b16 will already typically be approx $2,000 higher due to the cost of the swap, mounts, linkage, axles etc. Invest that money in a D, and dollar vs dollar the b-series cant keep up.

N/A can be quick too, my other EF (when owned by its previous owner) ran 12s on a d16a6 N/A.