Yes, you can correct any rotation and translation values when post processing in LiDARMill. In the Navlab pipeline, ensure that the IMU to Antenna lever arm offsets and the Body to IMU Rotations are corrected. In the Spatial Fuser pipeline, ensure that the LiDAR 0 rotations and translations/offsets are corrected. Camera rotations/translations can also be corrected if applicable.
If you don't have these values handy, the correct values could be obtained from past project reports and trajectory reports from pipelines you've ran with the desired profile.