If you ran a pulse-matched manifold to each I would think a balance pipe would completely ruin the whole point of it.
The main thing with actual twins versus compounds is that with actual twins you move a lot of air but the pressure ratios aren't that high. At what PSI does a 351 get towards the edge of it's map? Since we have such crappy airflow in our engines the go-to move is just to throw so much pressure behind the valve that the air has to get in there. Compounds are much more capable of getting the pressures up that high.
You may see twins on some full-out racecars and stuff, but they're had their heads, intakes, cams, exhaust, anything involving airflow really worked out so well that they don't need extremely high pressures to get the air in. Even if they could get more power from compounds they'll see diminishing return with the weight and complexity added.
I'm not going to say it won't work, it will and it'll probably look pretty cool to boot, but for a vehicle with stock heads and stuff getting your pressures up is probably a better way to go about it.