I thought that gamecube disks were still shown in the non-gamecube Wiis, since it's still the same 4.3 menu running on it that would be running on older systems. So I wouldn't worry about that.
I'd still say as long as the guide is followed carefully and exactly, it's a relatively safe process. The risk increases as people start fooling around with things off-guide on their own. Which is what I suspect happened to the first Wii. It wouldn't have been letterbomb that bricked it, but something else that he did that he shouldn't have.
Mau and some of the other veterans of the site may know if there is a way to tell if the motherboard came from an older Wii or newer Wii, but I'm not as voiced at how the hardware works as others.