As long as you have a backup there is not much difference apart from Boot2 installation of Bootmii is more robust than an IOS.
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The Wii has two processors -- an ARM core (inside the Hollywood, known as "Starlet") and a PowerPC (Broadway). The boot process starts on the ARM, which eventually bootstraps the PPC.
The code components involved in the Wii's boot process are, in order:
* (ARM) boot0 A mask ROM (1.5K) which loads boot1 and verifies its SHA1 hash against that stored in OTP. If there is a mismatch, the system will halt.
* (ARM) boot1 Lives in the first block of NAND; loads one of two copies of boot2 from blocks 1-7 of NAND and verifies it using RSA / SHA1.
* (ARM) boot2 A stripped-down version of IOS. It reads the NAND filesystem to load the System Menu's IOS
* (ARM) IOS sees its being booted thanks to the (lowmen?) writes of boot2 and bootstraps the PPC to start the System Menu title (1-2)