Apple's a large company, and like many large companies different people use different things ;) Since teams are largely autonomous with regards for tooling, I am sure that the choice of Homebrew or MacPorts for dependency management comes down to the choice of one engineer from the early stages of a project. For teams that use neither themselves developers are free to choose either for their machines. I would assume that new hires mostly pick Homebrew to use when given the choice.

I'd assume any sufficiently large and old MacOS shop uses some combination; I don't see why Apple themselves would be any different.