Guys I appreciate your quick responses.
So the problem remains- backup vs cloning, with pros and cons.
It's painful to see Clonezilla not being able to take out empty spaces while doing the .img thing. And DD is fraught even with a Linux laptop.
Question: Is the /storage folder the only one physically on the SD card?
How about /flash? I am assuming all LE folders are on SD card, or Clonezilla etc wouldn't be able to backup a complete image?