I've spent quite a lot of time getting to grips with Agisoft and have been making some good models. I'm using data from a road based survey. I am supplying the model with x,y,z and yaw pitch and roll. I've also supplied it with camera calibration and told it to fix calibration. I don't use the "optimise alignment" process as I don't want to to change any alignment and I I set tie points to 10,000.
I'm reasonably happy that my input values are correct - when I use these to make a model using alternative software (e.g. a trial license of Acute3d), then the resultant model is perfectly aligned with the LiDAR data.
However, the Agisoft model seems to be suffering some rotation - on one side of the road the mesh is about 20cm higher that the LiDAR data, and on the other side of the road, it's 20cm lower.
I tried using different Yaw, Pitch Roll values as a test and the resultant model was the exactly the same. Does it actually use Yaw Pitch Roll?