When you get invited under express entry, you will be required to undergo upfront medicals. The panel physician will ask if you have a preexisting condition and whether you are on any medication. You will be asked to provide a specialist report which should contain a 5 year prognosis including pathology and other diagnostic reports (colonoscopy/endoscopy if available) and treatment recommendation. The panel physician may refer you to a specialist or CIC could ask for further tests. I suspect you are in Canada, to circumvent any unnecessary delay, get a report from your GI doctor that contain the information the panel physician wants (you can find a specialists referral form online to have an idea of what your doctor should include in the report) and take it with you to the panel physician. Since the your Canadian specialist is certified by the royal college, his/her credibility would not be in doubt.
You need to sit down and have a deep meaningful conversation with your specialist, underscoring the importance of his report on the outcome of your PR application. Since you have been newly diagnosed, your specialist can only give a generalized prognosis based on the result of your colonoscopy and pathology reports which could be really conservative. IBD could take different trajectories from mild to severe. Overall, your specialist has an ethical obligation to give a honest report, but they always hope for the best case. Good luck.