Short answer: compression ratio doesn't change with the amount of air brought in. That is dynamic compression, or just cylinder pressure that is affected. Static compression ratio is the total volume of the cylinder at BDC divided by the total volume at TDC. So, increasing the stroke but keeping the same compressed volume will increase the compression ratio.
Long answer: If you have an engine cylinder which displaces 1000 cc (one liter) at BDC and 100 cc at TDC, you have a 10:1 compression ratio. If you increase that BDC volume to 1200 cc with stroke but keep the same compressed volume of 100 cc, you have increased its static compression ratio to 12:1 In order to retain the same compression ratio, you need to increase the combustion space at TDC by 20 cc in this example.
The amount of air that the engine actually ingests depends on RPM, cam event timing, intake design, throttle position, and dozens of other factors. Which means the actual pressure inside that cylinder varies widely based on those factors. Now we're talking about VE or volumetric efficiency, which is basically a percentage of mass. If an engine is operating at 100% efficiency, that means at BDC of the intake stroke, the mass of air inside the cylinder would weigh the same as the mass of an equal volume in ambient air. That is to say, the cylinder has completely filled based on surrounding conditions. When the intake valve closes, there is neither negative nor positive pressure in the cylinder. In truth, most street engines operate between 75-90% VE and naturally aspirated race engines usually operate at a peak VE of 80-100%. Forced induction engines actually operate sometimes well over 100% VE since they are receiving pressurized air. Its also important to point out that when I speak of those VE numbers, I'm speaking of their peaks at WOT. On a dyno at WOT, those peak VEs occur at an RPM where airflow is maximized by the wonderful selection of matching parts you've chosen for your application. This is why mismatching parts hurts engine performance so much. Using an intake that tunes peak VE for 3500 rpms, but a cam that tunes it for 2500 rpms means they will never work together to make power at the same time... but I digress.
So what I'm saying is basically, increasing the static compression ratio makes a general, across-the-board shift upward in peak cylinder pressures (all other things equal). In your example, the stroked engine would ingest more air and compress it into the same size combustion space. This is the exact premise behind why hotter cams require more static compression ratio; Hotter cams allow bleeding of cylinder pressure at lower RPMs. Increasing the static compression raises the actual cylinder pressures back up to recover that lost pressure. Without that cylinder pressure, large cams make wimpy torque down low in the RPMs.