You must use dd to Backup the Contents of the mtd Devices. Because those are the ones containing everything.
In case you brick your Device you can use that Backups to reflash the ROM. If you brick your Device and it won’t boot at all, then you would need to desolder the SPI Flash and flash the Contents of your Backups.
But WD always has two Bootloaders in their Flash based Drives. The Recovery U-Boot loads first and checks the Flash and the GPIO’s for a Button Press. If everything looks good then the second U-Boot gets loaded and starts the regular kernel with the regular Root.
So unless you do not touch the very First Sectors of the Flash you should be good. The internal Flash is to small to hold a good Base System of Gentoo or Debian anyway. So the only thing you would need to tinker with would be the second Stage Bootloader and the Kernel in order to start your Base System from HDD or preferably from SDD.
You can leave the original Root FS as it is in order to have a Fallback Safety when things go wrong.
