It is confusing, I know. Apparently, it is possible to finish the program with a master's if I leave in June. I know this seems like a relatively fast way to get a master's, and I don't know why this is so, but that's how it is. So I wouldn't be transfering from an incomplete master's degree to MD/PhD, I would be leaving my PhD program with a master's before matriculating to an MD/PhD program. I originally wanted to transfer from my PhD into the same school's MD/PhD and work for the same PI, as you said. When I realized I can't "transfer" but have to go through the same process as everyone else, I decided to apply to a few additional schools anyway, to see what they say.
I have done 16 months part time research while in undergrad, and 6 months (2 summers) full time research in the pharmaceutical industry, 36 MCAT, 3.95 GPA. I wish I would have known to apply to MSTP last year, then my life would be a lot less hectic