I think that yes, you can load the program and save the image to the CF card even if the I/O is different.
The CPU has to be the correct model (1769-L32E, not a L35E or L43, for example) and the firmware revision should be the same as the target.
Once you've created the binary image you can transport the files any way you like; you could e-mail or FTP them and have the guys onsite put them onto a CF card.