Thank you so much for informing me.
That was what I finally ended up doing, going through an existing project's init procedures by debugger, noting down all settings, and then reproducing them in CubeMX, so that now I can add functionality there.
Thought there might be a more simple way such as compile the existing project, start it in debug mode, stop after init, and have a tool read the config registers and store the information as an ioc file, which unmodified would create code to reach the same init state, or after being modified in CubeMX would add more functionality to the project, while all can be maintained in CubeMX.