I'd say the most plausible scenario is that the update warning about modded consoles is the new standard message that appears when you try to update/run a update, meaning that it will pop up for each update from here on. (Hence the reason why it only appears AFTER the 3.0 update has been installed.)
This is probably just a safeguard so that they don't have to have a million kiddies cry to them after bricking their wii's after running a different-region update from disks, which happened on the super paper mario update and so on.
I'm curious about the modchip update disks not working though, if the wiikey team gets their fingers out of their asses soon, I'd atleast wait to update before you've run the wiikey update that's coming up eventually. (Since people have allready confirmed testing out the beta).
ALSO. If all else fails, you can always reset your console back to factory settings. Wouldn't that remove updates too? Or is it flashed onto the thingie? If that's the case, this update better fix my Wii, my channels are all f'ed up after a crap ntsc update on my pal wii. Heh.