Once Linux is running, firmware upgrades happen by writing to a /dev/mmcbllkpX device. There are more partitions than just the one holding the kernel, you will have one possibly holding the initrd or rootfs, and one acting as the "NVRAM" or holding settings. The bin file is probably designed to be written to a flash partition directly, then unpacked/loaded into RAM by the bootloader. This bootloader will load a kernel image and initrd from a partition of a NAND device, then run it. This bootloader is typically accessible via a serial port, but some platforms (like AR7) do weird things like have an FTP server going (you can flash firmware through it). Most MIPS/ARM based routers have a ROM bootloader that runs when the device is powered on.
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