I would be more concerned with brinelling (fretting) the aluminum heads using a thin steel gasket. Airflow Research recommends the Fel-Pro 1003 with their heads on a 350, so that's what I would use on AFR heads. They're 4.166" X 0.041" and you're correct, the squish won't be ideal until you cut the decks for zero piston deck height. Will you get by with it? Yeah, with aluminum heads and 9.65:1 SCR. Will it be as good as it could be? No.

David Vizard runs his motors at 0.035" and has said that he picked up power all the way down to that point. I suspect he would go tighter yet, but might be concerned about experiencing a piston/head collision.

You didn't say the manufacturer of your heads, but bottom line, use the gasket recommended by your cylinder head manufacturer and tailor other engine parameters around that (like cutting the decks for better squish).