Hello Eduardo,
Here is a sample script that rotates model coordinate system in accordance of bounding box for active chunk
#scale is kept
#compatibility: Agisoft PhotoScan Professional 0.9.0
import PhotoScan
import math
doc = PhotoScan.app.document
chunk = doc.activeChunk
R = chunk.region.rot #Bounding box rotation matrix
C = chunk.region.center #Bounding box center vector
if chunk.transform:
T = chunk.transform
s = math.sqrt(T[0,0]*T[0,0] + T[0,1]*T[0,1] + T[0,2]*T[0,2]) #scaling
S = PhotoScan.Matrix( [[s, 0, 0, 0], [0, s, 0, 0], [0, 0, s, 0], [0, 0, 0, 1]] ) #scale matrix
else:
S = PhotoScan.Matrix( [[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0], [0, 0, 0, 1]] )
T = PhotoScan.Matrix( [[R[0,0],R[0,1],R[0,2], C[0]], [R[1,0],R[1,1],R[1,2],C[1]], [R[2,0],R[2,1],R[2,2],C[2]], [0,0,0,1]])
chunk.transform = S * T.inv() #resulting chunk transformation matrix