But with Android, the choice is between your OEM overlords and the Google anti-fragmentation efforts overlord. Yes; you can flash your own ROM and switch to CyanogenMod or Replicant. That is the freedom you are guaranteed in Android. But how many people actually take advantage of it?
I take advantage of it. I love it that I can take advantage of it. I also helped about 5 other people take advantage of it, by installing Cyanogen on their obsolete phones (I'm not from the US and down here people keep their phones longer than they should).
What you say is a classic logical fallacy. Do you repair your own car? Personally, I like having the freedom of doing repairs on my car outside of "authorized" repair shops, even though I know nothing about cars.
You forget about "Unknown sources". In practical terms that is substantial freedom (see: Amazon and other app stores) that makes Android phones qualitatively different from phones with an overload (OEM, carrier or otherwise).