Sorry for the late response, did you solve this problem yet?
It seems like you were trying to do the cropping from the command line of the sample_multi_transcode application, I did some investigation on the following document but I can't find it:
To do the cropping, the VPP--video post-processing function must be used in the video pipeline. You might look at the following article to add it into the code yourself:
Hope this helps and let me know if you have any further questions.