They do own 49% [1]. So, sure they are separate organizations. But, when someone owns 49% of your house they have some sway in the decision making that happens. When you look at this from a integrations standpoint, where MS is going to have this baked into all their products, you can expand this logic way more. They are for sure influencing roadmap in areas they are interested in.

[1] https://www.theverge.com/2023/1/23/23567448/microsoft-openai...