The Python API has a method chunk.exportMarkers(), and also a method chunk.importMarkers(). So those should probably work. But it seems like what you really need is a way to automatically detect the markers in the 2nd model, so that you can automatically align the 2nd model to the 1st one.
Assuming you're not using PhotoScan's auto-detectable markers, it seems like the best thing to do is manually locate the markers in both models, then chunk.exportMarkers() from both, and do whatever analysis you would like to compare the two sets of coordinates.