So I am trying to keep my engine all tuned to the correct intake to exhaust cfm on heads and I am trying to figure out if compared to the stock manifolds and stock exhaust, if headers and a tuned length exhaust increases the cfm on the exhaust side of the heads. Its a hotter cam 305 and have the intake fully ported and a bunch of other aftermarket things. But before grinding on exhaust ports I wanna keep the intake to exhaust under 70%

 

If the header is built to the motors requirements for exhaust size then it will have an increased effect on extracting flow from the cylinder during blowdown. It will scavenge more, pulling on the charge which helps draw new intake air in.
Head port isnt changing in physical form. You are just getting more out of it by exhaust tuning

Now on a flow bench, perhaps pipe size and shape may show different flow numbers for the port, just like on the intake port size, different radius bell mouths vs clay inlets etc all have effects on the cfm you measure.