I found the reason that the images & clones do not work when done from the flash drive.
USB Flash drives mainly consist of USB controller chip and flash memory.
The virtual CD drive is written to the controller chip by the utilities like UFD Utility .
The image or clone of the flash drive is done of the flash memory only .
I don't know how the controller chip contents might be viewed so you might have some example of whats there.
I think what you are going to need to do & I've never done it so I don't have instructions.
You need to partition the external HDD. One partition needs a virtual CD drive that uses CDFS . It then needs to mount the .iso containing the autorun.inf & batch files you want to run. If the .iso or other image file can be left mounted then it might work better.
I appeal to other members that have a better knowlege about this to jump in & help .