The test is for latent TB, although it can be confused by previous TB vaccine immunization.
The difficulty of identifying TB is a problem, but it does move around the body and one of the subjects in the papers you link to was diagnosed by culture of a lung sample which appeared after serious damage was done to the ileocecal valve. There are visible traits that identify lesions of TB and although there are false negatives in a significant number of culture tests, it is not so rare that it would be outside of a pathologist's experience. Even the US sees a rate of TB that is about
40 per 100,000 each year, or 120,000 cases per year nationwide. One other trait that TB has is that intestinal lesions appear to be like lesions associated with bowel cancer. This is rarely true of Crohn's.
TB is more a problem for people with some immune compromise, which is why they test for latent TB before starting therapy with immune suppressors. Info on Wikipedia suggests that 90% of people with TB show no symptoms (latent TB) and of those, only 10% will progress to TB in their lifetime (See: Wikipedia