I find the intake usually kills off some flow.

I “usually” only bother flowing the intake to see how much it’s dropping the head flow.

Occasionally, if I’m having trouble with the port “backing up” at high lifts, and can’t seem to cure it...... I’ll put the manifold on and see if it helps with that trend.
Sometimes it does, sometimes it doesn’t.

The “fixed orifice” type of bench(what mine is) are much less affected by weather than the “laminar flow element” type bench.
The FO type bench isn’t trying to determine what the actual flow is...... it’s comparing the head to an orifice with a known flow capacity..... and the weather on both “sides” of the bench(inlet and outlet) are always the same as each other.

I had my old SF-110 for 14 years...... and the bench correction factor never changed. Warm, cool, humid, dry........ the test plate always flowed exactly the same(same reading on the manometer)......... if you did the test the same way.