This. There is also absolutely no compelling reason to remove the original meshes from your list afterwards anyway. You will need them when you next make a change and need to re run ParallaxGen.
I think there may be some misunderstanding of how the tool is actually used. It’s to patch your existing modified meshes to add flags. The only reason that the mesh is duplicated is because it’s been patched. It’s pretty nonsensical to think you would then use this patched output standalone in some way.