The strongest engine I tested those two together on was my 427 dyno mule. Peak torque for the Ford and Blue Thunder manifolds was very close, 527.8 lb-ft for the Blue Thunder and 526.6 lb-ft for the Ford manifold. However, the BT manifold was a little better on HP, 596.9 vs. 577.8.
On my 390 stroker the differences were much less pronounced, 512.1/517.7 (torque/HP) for the Blue Thunder, and 516.8/517.7 for the Ford. The Ford manifold was actually a little better on torque than the Blue Thunder manifold, on that engine, which makes sense if the internal passages of the Blue Thunder manifold were bigger. And they were exactly the same on horsepower, which is rather remarkable...
Neither intake was port matched for these tests, but the Blue Thunder intake did have larger ports. Port sizes were 1.22" X 1.92" for the Ford, and 1.35" X 2.09" for the Blue Thunder. That was at least a part of why the BT intake was stronger on the higher power engine, and could be the whole reason.