From my experience with Dolphin's GCZ compression:
In other words, if your Wii ISO had the MD5 of a good dump before compressing it to GCZ, don't worry, its MD5 won't match anymore after decompressing but the game files will still be intact (you can confirm this by right clicking a partition and choosing "Check partition integrity" through Dolphin's Game Properties).
And about comparing the MD5 of a plain ISO vs a compressed ISO, as long as you use recent development builds (and use Dolphin's built-in "calculate MD5 hash"), Dolphin should return the MD5 of the uncompressed ISO, independent of whether it's compressed or not.
- GameCube to GCZ compression is lossless. Same MD5 of the original ISO after decompressing the GCZ file.
- Wii to GCZ compression is somewhat lossy. The files inside the ISO will remain intact, but the unused spaces will be scrubbed.
In other words, if your Wii ISO had the MD5 of a good dump before compressing it to GCZ, don't worry, its MD5 won't match anymore after decompressing but the game files will still be intact (you can confirm this by right clicking a partition and choosing "Check partition integrity" through Dolphin's Game Properties).
And about comparing the MD5 of a plain ISO vs a compressed ISO, as long as you use recent development builds (and use Dolphin's built-in "calculate MD5 hash"), Dolphin should return the MD5 of the uncompressed ISO, independent of whether it's compressed or not.
Avell A70 MOB: Core i7-11800H, GeForce RTX 3060, 16 GB DDR4-3200, Windows 11 (Insider Preview)
ASRock Z97M OC Formula: Pentium G3258, GeForce GT 440, 16 GB DDR3-1600, Windows 10 (22H2)
ASRock Z97M OC Formula: Pentium G3258, GeForce GT 440, 16 GB DDR3-1600, Windows 10 (22H2)