D15B in 5th and 6th gen Civics is faster than D16W9 in 7th gen one only because those are lighter and have better traction, thanks to superior suspension.
It's not right to think that D16W9 is inferior or less powerful. The whole 7th gen package, car+engine, is slower than the earlier ones though.
That theory has its merit only for pre 7th gen Civic. 7th gen D15B is not for power, it's a VTEC-E motor.
Higher Japanese quality? You do realize that all the engines are made in Japan anyway? And for the record, D16W9 is better motor, and more powerful, than its Japanese D15, D17 counterparts.
D16W9 IS 3 stage VTEC- similar to those Japanese D15B 3 stage in older models- only BETTER.
Small mods like what? I think it's right to believe that there's no replacement for displacement, even if it's as little as 100cc. That said, in a similar car, D15 cannot kill D16.