I don't know anything about their treatment, but their premise is correct.
Inflammation in crohn's disease is present in the ileum and colon where the bacteria are. It does not happen in the duodenum or jejunum where bacterial loads are meaningless. These bacteria and bacterial metabolites are not all harmless, the intestine has to be permeable to allow entry of nutrients, so it is in a constant struggle to try to maintain a type of homeostasis. The sheer number of TLR, macrophages, paneth cells, peyer's patches in the intestine and the constant turnover of epithelial cells show this struggle is a daily battle, even in healthy controls.
People or researchers who have any doubt about this, should look at the differnces between animals with resident and transient microbiomes. The potential of resident bacteria to cause intestinal injury is vastly underappreciated.
Genetic anomalies, defective macrophage handling and delayed neutrophil recruitment indicate there is a problem in crohn's disease patients, leading to innate immunodeficiency. EN reduces bacterial load and contact of the fecal stream with the epithelial barrier leading to healing, indicating you can intervene before inflammation happens and before these deficiencies manifest themselves.
Current treatment is a step behind, they try dampening the adaptive response by blocking inflammatory cytokines after the inflammatory cascade has already started, this is not a great or sustainable solution for patients. Many fail on these types of medication, and it is not curative. It stops the destructive nature of inflammation, but it doesn't address the source of this inflammation.
So you need a way to be a step ahead, intervene before the inflammation happens. EN does this, but there is a wide open field of other types of treatment that could intervene before inflammation occurs, by intervening in the events leading up to it.