The intake valve should be opening towards the end of the exhaust stroke. Then the remaining exhaust push will help create a vacuum to start the intake charge early and fill faster. Is this what you mean?
What's the pressure in the chamber when the intake valve opens? Theoreticals are not realities.
Anytime you create conditions that invite reversion like bigger valves, bigger runners, bigger intake bigger carb and longer duration camshafts then you are not filling the cylinder no matter what theoretical air flow or velocity you measure on a steady airflow bench. Exhaust gases usually are innate but if you're making lots of CO during the burn that's a burnable gas that requires energy to burn again and that's diluting the next intake charge when it heads back towards the intake valve