I figured it would be a "huge red flag" too, but I applied anyway. I even applied to (and was accepted to) schools that said outright that people in PhD programs would not be considered until they received their degree. I indicated on my AMCAS that I was in a PhD program but would leave with my masters if I got accepted to medical school. I figured it would be held against me but they invited me to interviews anyway. Afraid they had just missed that detail, I was sure to remind them of my situation but none of them were concerned, they told me they understand the change in heart and didn't see it as me abandoning research since I full well intend on pursuing research regardless of my final degree(s) being MD or MD/PhD.
For my GPA, it was a simple case of a family crisis during my sophomore year that caused a hiccup in an otherwise impeccable undergraduate. I explained it on my personal statement, and during my interviews they told me they completely understand, and have no question in my aptitude or intelligence considering my MCAT and that since my sophomore year I've had nearly 80 credits of almost 3.8GPA undergraduate coursework, all of which were upper level science courses. This was in addition to my 4.0 Graduate work, attained while studying for MCAT, shadowing, and doing my research. I was also told by my interviewers that my 5 letters of recommendation were some of the most outstanding they've received in years.
For the MD/PhD, I didn't say I was accepted, rather that they are pretty interested in me; and they are. I have interviewed and the process is going well, my performance in my graduate coursework as well as my laboratory performance has earned me a great reputation here and several of my collaborators are actually MD/PhD committee members fighting for me. While chatting with the MD/PhD director she actually asked me why I didn't apply to more MD/PhD programs, explaining that GPA may be higher for the "average" accepted student but that they were much more flexible than you read on the internet, especially when they have someone that is otherwise exceptional. She said I was what they called "Damaged Goods" meaning I would be screened out of the top MSTP/MD/PHD programs but non-top-tier programs would be extremely interested in me. I don't think this makes me guaranteed to get in, but it certainly means I've got a pretty good shot.
I've been holding off on explaining this in detail because I wanted to wait until all the dust has settled. I also fully understood many would not believe me, so I'll be happy to upload my acceptance letters once I do make a thread about it. I feel many misconceptions need to be dispelled here on SDN, things that may be generally true but certainly not gospel as it is treated here.
Back to the subject at hand, my advice is still the same. It has been extremely hard to do what I'm doing and have done and wouldn't wish it on someone who was in my shoes not too long ago.