Maybe it's not my place to suggest this since I imagine that the user-facing UI side of things is super unimportant in terms of bottlenecks preventing this from being implemented, but a checkbox labeled something like "repair for playing on real hardware (not 1:1 clean)" on the conversion window which itself would be always be greyed out unless you were specifically converting from extracted files (which Dolphin seems to already be able to know when this is the case as it always labels the file size of extracted files as zero).
Dolphin 5.0 CPU benchmark
CPU: Pentium G3258 @ 4.5GHz 1.24v
GPU: Intel integrated
RAM: 4x4GB Corsair Vengence @ DDR3-1600
OS: Linux Mint of some variety + [VM] Win7 SP1 x64
CPU: Pentium G3258 @ 4.5GHz 1.24v
GPU: Intel integrated
RAM: 4x4GB Corsair Vengence @ DDR3-1600
OS: Linux Mint of some variety + [VM] Win7 SP1 x64