Hello andyroo,
Do you mean, that the bounding box remains the same (for the whole area), whereas the dense clouds and DEMs are generated within much smaller area?
If you do not want to alter the bounding box for each subset, maybe you can try to use region argument when building DEM?
region = Metashape.BBox()
region.min = Metashape.Vector([x0, y0])
region.max = Metashape.Vector([x1, y1])
chunk.buildDem(region = region)