I have a mallory mount with a BHAF on it and have never had a problem with it getting wet. I drove in some good rain storms this fall and I checked the filter, it was always dry as a bone. I don't do river crossing with my truck so I guess I will never know if that would get if wet. If you are really worried I do not think it would be that hard to make a screen of some type that would fit on the end of the BHAF that could catch any chunks that came off the filter.
To answer you other question, I think you could use the mallory mount with any of the aftermarket filters. I had the KNRE0880 prior to the BHAF and I believe it Mallory mount would hold it in place just fine. All it would take is a smaller zip tie.
I could not get the link to carls website to work either, but the other link worked fine. Does any one have the part # for the BFF??