It's probably not a great idea to take the MCAT during the BMS program. Not impossible, I'm sure people have done it, but from my experience the program was so rigorous that I don't think I could have done well in both the program and the MCAT. The linkage is only good for your time in the BMS program, so if you finish the year, take the MCAT after and apply to CMS, you'll be treated as an outside applicant without the benefits of BMS. This program is absolutely high high risk and high reward. I wouldn't go here if you can't absolutely commit during the whole year to crushing your academics without distraction. If you do, you've got a decent shot at an MD school. If you don't, you're over $50,000 deeper in debt and have significantly lowered your chances at admission since a subpar SMP doesn't look too great.
From what we were told, once you're in the program your old GPA and MCAT don't matter, just your performance here. Is that true? I can't guarantee, since I'm just a student and I'm passing down what the CMS admissions faculty have told me when I asked them. Regarding other med school connections, I have absolutely no clue. Maybe, but I haven't heard of any so I would put too much hope in linkage with anything outside of CMS.