I'm pretty sure your registration priority is based on your credits, and is no different for Junior transfers than junior traditional students. If you can get in to at least one of the two classes, then you could look at simultaneously doing MCAT prep while taking the other as a summer course. I did this with summer Physics + MCAT prep, and it went well, I just saved the physics content review for last so I had covered almost all of it in the course and only had to learn a few things from the study books.
And yes, tiny LACs tend to have a lot less overcrowding, especially in BCPM, relative to large and/or public universities. I'd call the large university(s?) you're considering to find out what sort of waitlist is typical for bio and physics, and if it often fills up with upperclassmen and has a long waitlist (seen all the time in my U Cali system where it can be hard to graduate in under 6 years) then look at small LAC alternatives.