Thank you for the response CMata_Intel.
What if I wanted the files in /home/root deleted as part of the flashing process? Is there another command other than reboot ota? Obviously, I can remove any files manually, but is there no way to restore a clean image? I did a bunch of trial and error when setting up the module for the first time and I was hoping to go back to a clean (more or less factory) image.
When you OTA the only thing, which is preserved is the contents of your /home partition and that's by design as far as I can see in the sources (you can see that yourself if you're up to that - check out the BSP in the Downloads section).
Everything else (i.e. the actual OS) is rewritten. I think the idea of preserving /home is that you might have some data or configs you've created during tinkering and erasing them during firmware updates (forcing you to back it up first - and imagine if you forgot and that was the only copy) would be too inconvenient. Actually in early images it was rewriting everything and /home preservation appeared later, probably based on the user feedback.
Be sure if OTA succeeded you have a clean system and if you want to remove any possible root user-level configs, just delete everything under /home/root (but not the /home/root dir itself).