There are other and very important possible reasons for the initiation and the chronicity of the intestinal permeability problem other than microorganisms. Some examples are the immunogenicity of the foods and liquids we consume, endocrinological state of the person (this is quite complex but the easiest you can look for is the direct relationship between elevated cortisol and the increased intestinal permeability), the energy metabolism of the person etc.
Fully elemental EN works, because it is not fermentable (massive reduction in the microbial load) AND it doesn’t contain immunogenic substances like casein; unlike non-fully elemental EN like modulen, which is casein based. Even if, theoretically, you get a sterile gut, if you keep putting immunogenic substances on your mouth and swallow, the inflammation will continue, though it will still be decreased a lot because of the non-existence of the microorganisms.
Fully elemental EN are amino acid based.
I agree that claims and speculations about good and bad bacteria are bogus. Microbiota topic is highly complex with its interrelations with each other, the host, the environment, epigenetics etc. And the current knowledge about the topic is almost nil - compared to what needs to be known.
Surgical diversion of the intestines is also effective, for the same reason: limiting the microorganism growth and stopping the immunogenic foods’ stream, also toxins in our foods, drinks etc. Not surprisingly, often quickly after the reversal of the diversion (anastomosis), crohns returns in patients.
Edit: fully elemental EN is quickly, efficiently and easily absorbed in the small intestines. That’s what I mean by the “not fermentable”. Compare it with starch for the fermentability issue. By the way, because of these, your nutritional and hormonal state, and energy metabolism improve from fully elemental EN. Which are also relevant mechanisms.
Edit 2: also, with the exclusion of hard, irritating, fermentable foods, intestinal serotonin decreases a lot. This is also relevant for the inflammation, functionality, healing. People with Crohns have elevated serotonin in their intestines.