A clinician uses profesional judgment to decide what diagnostic tests and treatments to order. A protocol takes that judgment away from the clinician and dictates to the "investigator" what is to be done at each visit. There isn't anything "not good" about it, but it is not clinical care, it is research. The protocol says you'll have a CT scan at 3 months to measure progress and that is done as part of the protocol. It isn't a clinical decision and there isn't a conversation with the patient about why it is done, just the research participant's agreement to undergo the procedures listed in the protocol and described in the consent form.
Some people may consider it clinical care but some will not. You don't want to get caught with insufficient clinical experience because by luck of the draw you ended up having your application reviewed by people who took the more narrow definition of clinical care.
it is very, very rare for a person with a BS degree to get a publication from a clinical research study. The only time I can remember seeing such a thing, it has been a medical school professor's kid.
YMMV but you need to go into the application cycle knowing how these things might be perceived.