1. Applicants get way, way, way too focused on a single metric like GPA. While UG sGPA (BCPM) is the primary metric as it has at least a very rough standard across all applicants, schools will take into account grade trends. post-bacc, SMP, and, to a much lesser and widely varying extent, other graduate GPA. However, this is specific by individual school and all schools will at least screen AMCAS Primary beyond a formalistic calculation of metrics
2. With such a low UG GPA and such a highly improved grad, post-bacc, and MCAT metrics, you need to address this VERY BRIEFLY in PS (in less than 1 sentence) and make a statement that your grad/postbacc GPA and MCAT are much more representative of your academic ability. You should have used this "effective" GPA and MCAT when targeting schools
3. I am more concerned with leaving a PhD program. Medical schools look for a pattern of motivation, commitment, and achievement, and you are weak on all three. This is especially true of commitment: if you weren't going to stay and finish a PhD you decided to start, how can they be sure you will stay and complete the lengthy and arguably more difficult training of medical school and residency.