A couple of years ago, there were a number of posters who applied MD/PhD to schools after initially applying only to MD programs.
If I remember correctly, those posters said that when they designated their first MD/PhD school, the additional essays opened up and they were able to complete them. Several people verified this.
However, I have not personally tried it, so this information is secondhand. Also, that was a couple of years back, so I would try to find someone with more recent info before banking on it.
Also - regarding applying to the PhD program internally - ABSOLUTELY check with the individual schools before you plan on this. Some allow internal transfers but don't have room unless a current student drops out. Other schools specifically set money and PhD spots aside for MD students. You need to know which class a school fits into before you apply internally.