The first step would be to modify the game ID right at the start of the .iso with a hex editor. I'm pretty sure this is what Dolphin uses to decide where to save etc. and hence it'll be the way to make it not think everything's the same game.
OS: Windows 10 64 bit Professional
CPU: AMD Ryzen 5900X
RAM: 16GB
GPU: Radeon Vega 56
CPU: AMD Ryzen 5900X
RAM: 16GB
GPU: Radeon Vega 56
