OK, it was independent but established with funding from YC Research and Jessica (among others including Sam himself and Elon) and initially operating from YC office space.

So it was always something that was closely linked to YC and his involvement with it was generally accepted as being harmonious with his role running YC, until it became for-profit.

Details here:

https://www.wired.com/2015/12/how-elon-musk-and-y-combinator...