In that case, I'd recommend the following options -- both of which are more straightforward and less prone to errors (including the potential to have catastrophic loss of data/functionality if done wrong):
add those areas to the backup. Anything you put in /etc/sysupgrade.conf will be included in the backup.
copy your custom files/configs and build an image (using image builder) that includes all of your files and even the user-installed packages.
If the only acceptable method for you is still to try to close the actual flash storage, hopefully someone else can help (I would, but I'm not an expert in that particular method).
The custom image is probably the fastest and easiest to restore, actually. It is pretty close to a clone for practical purposes, but requires less work to install.
Anyway, hopefully someone else can chime in about how you can clone your system.