Back to my normal profile... (not sure how how my work PC was still logging in with old profile) As far as python goes I'm pretty much a noob but I've got a script working for most of the process.
import PhotoScan
import math
doc = PhotoScan.app.document
chunk = doc.chunk
# Detect markers
chunk.detectMarkers(type=PhotoScan.CircularTarget12bit)
# Load reference
chunk.loadReference(path='markers.txt', format=PhotoScan.ReferenceFormatCSV, columns='nxyzXYZ', delimiter=',')
# Align images
chunk.matchPhotos(accuracy=PhotoScan.HighAccuracy)
chunk.alignCameras(adaptive_fitting=False)
# Rotate ROI to coordinate system: Bounding_Box_to_Coordinate_System.py
#rotates chunks' bounding box in accordance of coordinate system for active chunk
#bounding box size is kept
#compatibility: Agisoft PhotoScan Professional 1.1.0
T = chunk.transform.matrix
v_t = T * PhotoScan.Vector( [0,0,0,1] )
v_t.size = 3
if chunk.crs:
m = chunk.crs.localframe(v_t)
else:
m = PhotoScan.Matrix().diag([1,1,1,1])
m = m * T
s = math.sqrt(m[0,0] ** 2 + m[0,1] ** 2 + m[0,2] ** 2) #scale factor
R = PhotoScan.Matrix( [[m[0,0],m[0,1],m[0,2]], [m[1,0],m[1,1],m[1,2]], [m[2,0],m[2,1],m[2,2]]])
R = R * (1. / s)
reg = chunk.region
reg.rot = R.t()
chunk.region = reg
#END: Bounding_Box_to_Coordinate_System.py
Now I need to set the size/position of the bounding box between a CP for the top/left and bottom/right corners.. The steps after that I've got working (dense cloud, heightfield, orthomosaic).