If the NAND is being presented as mmc type device, perhaps the baseband ("radio") processor is performing mmc to nand conversion, and also acting as a gatekeeper? Don't the baseband processors often perform other interfacing functions in other devices?
This might also be relevant to the ~2.1GB mmc size weirdness - there are of course not going to be non-power-of-two NAND devices so all these ~2.1GB devices must have 4GB of space but may show up with an odd number of sectors due to gatekeeping by the baseband processor.
The baseband processor might simply discard any writes to certain sectors not being performed in an approved fashion (perhaps using special IPC calls or by first authenticating with it to enable write through). Perhaps it caches writes in the "rest" of the NAND space, until the next reboot?
Perhaps there is some kind of dual partition set up like a Tivo for the system partitions, so you write your OS update to the other partition set (through whatever nonstandard methods are used), write config someplace indicating to use the other partition set, reboot, bootloader tries booting and if things don't check out, revert to previous partition set.