Which engine is beside the point, which is pretty simple: the head with the better CFM flow may do something, nothing, or less than nothing when boosted, and there's no reliable way to predict this except empirically: what worked before will work again.
Another comparison: the LSX cathedral head (smaller port, now considered obsolete vs. the rectangle) appears not to matter at all in a small bore engine such as the 4.9 liter.
If I had to draw a conclusion: don't experiment with boost on the basis of comparative NA flow or dyno results.