When you just use MenuHax, the NATIVE_FIRM would still be fine and intact, but when you use CakeHax/Brahma/etc., which is what we use to launch CFW, you're doing a hostile takeover of the ARM9 CPU, so whatever Nintendo code was there will be trashed or removed. Even if you could still use the current NATIVE_FIRM, that wouldn't necessarily be desirable, since the 4.x-9.2 kernel is pretty old, and newer games are needing newer ones. I would take a guess that there would also be race conditions or stability issues with trying to redirect already running code to read from SD instead of NAND. It's probably much, much safer to load a new kernel into memory, patch it to read from SD from the get-go and then just reboot into it.