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.
So your saying add boost and see what happens.
Then open up the flow through the engine and see what happens.
If the right things don't happen, call someone who has made it happen.
