And what does it matter how the company is organized? YouTube is in fact a direct subsidiary of Google, not just a sibling company under Alphabet, but so what? Would calling it "Google Video" make a difference?
The problem with the earlier hypothetical example (of Spotify acquiring Medium and blocking articles about apps that violate Spotify's ToS) was not cooperation between Spotify and Medium, but issues regarding free speech, insofar as that applies to a private platform.
The analogous situation with YouTube would be content on Google platforms discussing third-party YouTube apps... and in fact, there are plenty of videos on YouTube itself discussing youtube-dl or apps such as NewPipe.
> Youtube isn't using legal means, in general.
That's semantics. Call it technical vs. non-technical means, then, or whatever.
The problem with that line of ideological reasoning is that it implies YouTube should use technical means, such as locking down its API, rather than just booting offending apps off the company's own app stores. The end result would be worse for users.