Nevermind, my mistake was, that I didn't see the variable existed under the advanced settings so I added a new one. But apparently my custom variable was overwritten by the default one. If I add the config file to the already present entry for the variable it works.
Is there any way to prevent MakeMKV from ripping a movie twice? It seems to create one file with and one without chapters, otherwise they don't differ at all so I'm not sure if I can filter this somehow in the auto ripper