I can only speak from personal experience, as I am not an expert in nutrition. The SCD has provided me a huge amount of relief from my IBS symptoms of gas and bloating, and motility. As I said, not a complete elimination of symptoms, but much more relief than when I was eating lots of starches (which is what I've done my whole life), or even when I spent several months gluten and dairy free.
The article you posted did have some interesting tidbits. It mentions the fact that the SCD hasn't been well studied because, unlike pharmaceutical studies, it is difficult to get funding. It's also difficult to create a control group to compare the effects. I am aware of the clinical trial. My husband is considering participating.
Another interesting thing in the article is that doctors agree that there may be subtypes of IBD, which explains why some people respond to the diet, and others respond to drugs. I think IBS also has subtypes. Most doctors in the article agreed that if the diet helped their patients, then it was worth a try.
The article does not accurately represent the science behind the SCD. It mentions doctors saying that the diet is contradictory, in that table sugar is not allowed, but fruit sugar is. This has to do monosaccharides (such as fructose) versus disaccharides (such as sucrose), and how they are fermented in the gut. The science of this process is well explained by the medical doctor who originally designed the Specific Carbohydrate Diet.
Finally, you mention that the SCD is nutritionally lacking in foods that convert to short-chain fatty acids. And, based on my research, all dietary fiber, including vegetables, fruits, legumes, and nuts, convert to short-chain fatty acids in the gut. There is no shortage of fiber on the SCD. You may be interested in this article on this topic.