The D3 drive and earlier had a built-in DVD mode for a potential DVD player channel. This mode was exploited for softmods and "flat" modchips to load burned discs, as they look similar to DVD-ROMs. The D3-2 drive removed this mode, breaking backup loading from disc.
Yes, Wii and GameCube discs are regular DVDs. Hence why Wii games can be burned to DVD-Rs.
Nintendo's discs (and rips of said discs) will not be recognized by Linux/Mac/Windows. If you ripped them, you would not get a standard ISO. The discs have a proprietary format, garbage data (to fill up unused space, this is why rips can be big), and a burst cutting area.