I faced a similar problem running a regular linux installation on top of a RS-MMC (damn slow, and too little for a regular linux distro)

I tried almost every solution available (unionfs, aufs, symlinked directories and so on) and finally I tried BTRFS with compression enabled and SSD mount opition.

The result is simply amazing, the system is incredibly fast, the bootime is almost a quarter than the one over a regular ext3 FS, and there is no space wasted as happens with the readonly fs overlaid by writable fs, trough aufs or unionfs.

So I vote for completely ignore the 256MB NAND and use a partition on 32 GB eMMC formatted with compressed BTRFS for the whole FS.

Eventually the 256 MB nand can be used for caching purposes, as suggested before.

The flashing problem can be eventually solved flashing not directly the emmc but the 256MB nand flash as happens now.

A script on the first boot can format the emmc partition and then copy everything on it (adjusting the configuration files when needed), so no worry for the user data on the vfat section.