No. Applying MD/PhD is a completely different animal...you have to do a couple extra essays on AMCAS describing your research and your reasons to pursue MD/PhD, and you have to have a certain number of letters from research faculty/PIs. This is something that has to be planned starting well before applying, not something to be changed halfway through the cycle.
Many schools allow students to apply to the MD/PhD or MSTP program internally (aka after you matriculate) if you decide that you want to pursue a PhD.
I'm not sure if every school does it this way, but if you apply MD/PhD, you are technically applying to both the MD program and the graduate program. If the graduate program rejects you, you can still be considered for the general MD pool.
No, I'm pretty sure it would need to be selected on AMCAS. The primary app is there to make everything easier for adcoms, so as a general rule - if it's easier for the adcoms, then that's what is required (for the most part).