At least for now, the geometry and the transformation matrix is not available through Data Exchange GraphQL API. The Data Exchange GraphQL API is still in beta and you have the chance to push for this feature by submitting a 3-5 minute feedback survey and suggest on Data Exchange Forum in what form you would like to receive this kind of information.

On the other hand, keep in mind that through Data Exchange .Net SDK you can get both, the geometry (in STL or Mesh format) as well as the transformation matrix for each element. For more info check this tutorial.