That's true, but 12 weeks isn't very long either. True healing can take months. That is really the limitation of clinical trials (or one of the limitations). On xeljanz I took 16 weeks to reach endoscopic remission. Histologic remission (normal biopsies) takes even longer.... in fact my doctor said 90% of patient in clinical/endoscopic remission will still show microscopic inflammation on a biopsy.
I have a J-pouch and my GI said that ALL j-pouches show microscopic inflammation even with no symptoms. He mentioned this to me when he said how great my J-pouch looked during the last scope. I have pouchitis and when untreated it develops ulcers. Treated with Stelara I had some of the least microscopic inflammation that he'd ever seen in any j-pouch.
His biggest gauge is how do his patients feel - blood work and scopes are helpful but they're not the most important factor.