The fermentation in the intestines is going to be from either food not properly digesting or more likely from overgrowth of yeast/fungi in the intestines. You mentioned taking probiotics, but you still need to feed the flora as well with fibers. Enzymes though often contain cellulase and hemicellulase that break down the fibers in to simpler sugars that feed yeast/fungi.
As for the absorption a simple method of increasing absorption and reducing the gas absorption is by taking yucca root. The saponins in yucca root increase cell wall permeability that increases dietary absorption. The saponins are also surfactants that reduce surface tension allowing the gas to dissolve in to the moisture and feces. Saponins also aid the intestinal flora. Sterols in the yucca root will help control the yeast/fungi.