I read in the GameCube ISO-ripping scene there was a big thing about whether to leave dummy files on the disc (presumably there for loading time purposes) or to cut them/replace with more compressible dummy data)
It's still debated in minor.
In personal tests, I've completely removed all dummy padding and aligned everything into 2048 byte sectors with perfect results on real hardware (both GameCube & Wii) and of course, Dolphin.
It also worked perfectly for games with especial audio/streaming, GameBoy Player hardware & other system disc data, Action Replay (must rename 4byte ID for Wii - something like "GAME", etc), promotional & prototype disc data, and everything else I threw at it.
In few cases, I noticed that some game titles ran slightly more seamless in demanding load times, as compared to retail disc/factory pressed counterparts.
Early on during testing, however, I noticed the key is aligning everything into 2048 byte sectors, so keep that in-mind before you quote me on anything