I think your daughter has a chance at the schools of her list; perhaps a lower chance at MIT. Her gpa and test scores should allow her to advance in the application process. Her accomplishments in chess, scouting and music demonstrate her dedication and talent. A paid science summer internship is a significant achievement. I am quite sure that she will be applying to other match and safety schools. I encourage her to apply, run her own race, be prepared for good news, as well as deferrals, wait listing and rejections. I suggest sending in the score from subject II math. Best wishes.
Rice and Vanderbilt might be more achievable targets/reaches (along with WashU) as opposed to Ivies for BME, especially with the high SAT 1.
Georgia Tech might be worth applying as well.
Final edit-Case Western is highly rated in BME/Biological Sciences. It would be a high match.