Except that in previous years MD-PhD applicants had to do the two additional essays anyway for each individual program. The inclusion of the two MD-PhD essays was the result of a request by MD-PhD program directors, who wanted to make it easier for prosepctive students to apply. The original goal was to arrive at a common application. This did not quite work out because some programs wanted to include a "vision question" (e.g., where do you see yourself in 15 years?) or a "personal question" (e.g., who is the person who has been most influential in your decision to pursue the combined degree), etc. In the end, the programs found two essays that were common to all applications; these are the ones that ended up on the AMCAS. For some schools, these may be the only questions they ask, in which case, you will not need to much else to apply to their program. For others, you will still need to answer a vision question or something else.
This being the first year that these essays are available on AMCAS, it is doubtful that many programs will be able to accept them. Programs will need time to figure out how to incorporate the AMCAS essays into their process. So, you may find that you will be writing the same essays for most of the programs you apply to. This will change in the coming years, but it will never be 100% since some schools can't or won't change their process. In the end, it is hoped that the majority of programs will accept the essays and make it easier for indviduals to apply to MD-PHD programs.
In reply to bottles999, only schools that you designate as MD-PhD will see the MD-PhD essays; schools designated MD-only will not see the MD-PhD stuff.