The foam material does breathe. The sound absorption is greater the higher the frequency, so the base port should be getting all the lower frequencies. I have changed the foam damping in my BL8000s to the updated version a number of years ago. The base response was not impacted. I use a pink noise generator along with a real time spectrum analyzer to adjust my system to be as “flat” as best I can. The lowest frequencies needed to be turned down a bit to get to “flat” response.
I think the foam materials and location info provided by B&O are just fine to use as-is.