good point about /home! on one of my ubilinux Edisons, I ended up moving/symlinking a service that tends to be lazy cleaning up after itself punctually, to the point it would often fill up root and cause problems.
I've never tried on a live FS, but there's technically a (safe) way with parted to reshape the partitions and have a soft reboot tidy it all up.
not sure if it could possibly be done in the flashall script - glancing at it briefly, looks like it's simply dumping images directly onto the metal.