Was able to do the same thing using the re-import feature by temporary overriding the project config file for one workstation using a bat script. Probably safer as well. Still interested to find a commandline solution for this. Will dig deeper by looking at https://github.com/EpicGames/UnrealEngine/blob/8e4560b8c22b309e73ff0ce90377742c3dfe13cc/Engine/Source/Editor/UnrealEd/Private/Fbx/FbxFactory.cpp