Alternative proteins are mostly for pets who have allergies, if your vet suspects IBD then the use of these proteins can help as allergies can cause this reaction in the guts.
chicken and beef are common ingredients that causes allergies so we try to get something the pet hasn't come in contact with yet. Allergies develop as your pet ages, for example if your cats have been on chicken based diets since kittens they can obtain an intolerance to it (though not always the case!).
This website has a really good summary of IBD worth a read - I'll add a few excerpts.
Chronic inflammation of the gastrointestinal tract can occur as a result of a specific disease, such as a parasitic or bacterial infection or a specific food allergy. However, the cause of IBD in many cases is considered to be “idiopathic” or unknown.
Some common signs of feline IBD include vomiting, weight loss, diarrhea, and lethargy. Appetite can be variable, ranging from ravenous to anorexic. While some cats will show obvious symptoms of disease, such as vomiting after every meal, other cats may exhibit symptoms much less frequently, such as vomiting or producing hairballs once or twice a month.
Making a diagnosis of feline IBD requires an extensive work up because many of the common symptoms of IBD, such as vomiting and diarrhea, are also common symptoms of other diseases. First, specific causes of gastrointestinal inflammation must be ruled out. Your veterinarian will likely recommend blood work, fecal examinations, radiographs, and/or an ultrasound check for metabolic disease, feline leukemia, parasitic or bacterial infections, and certain types of cancer. A hypoallergenic food trial may also be conducted to rule out food allergy.
Because dietary allergens may play a role in inflammatory bowel disease, a food trial using hypoallergenic diets may be recommended by your veterinarian. In using a hypoallergenic diet, the key is to use a protein and carbohydrate source that the cat has never eaten before. Rabbit, duck, or venison-based diets are often tried initially.
Cats that have been diagnosed with IBD may be put on a course of corticosteroids, usually prednisolone. Corticosteroids have potent anti-inflammatory and immunosuppressive properties. Diabetes and excessive immunosuppression are among the serious side effects these drugs can produce. Cats should be monitored closely while they are on corticosteroids, although they tend to tolerate these drugs well as long as they are given at an appropriate dose and schedule.
If your vet suspects IBD it's a good start to try out a hypoallergenic food however you can always get a second opinion if you have doubts.