I have worked on several projects like this before with some good and bad outcomes. From an engineering point of view, this can be a pain if the work culture and engineering processes are different in both companies. Also, if there are intellectual properties that one or more companies are trying to protect during this collaboration, this can make the process more cumbersome.
So to answer your question and based on my experience, it’s not so much the org structure that has impacted efficiency during collaboration, but more so processes, working culture and skill sets.