it’s not a valid comparison really. this is an alternative to an emulator than a ROM.
If you used this to compile a native version of space invaders that ran incorrectly it would be no worse than if you used an emulator to run space invaders that ran incorrectly. in either case you treat it as a bug in the emulator/recompiler and fix it and re run the process.
Nobody is suggesting deleting their roms and keeping only the current copy of a recompiled game. I don’t think that would even work… as far as I know you still need the original ROM to load inside of the recompiled executable for the non-code assets.