If the goal is getting smaller files (e.g. without changing game data), it's probably easier to use Dolphin conversion features to compress the source file to GCZ, or preferably, RVZ. If you want to actually edit the ISO contents, I would suggest using WIT instead to do the modding, then optionally compress the final file via Dolphin...
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)