That is definitely (mostly) true, but integrated engines like Unity or UE4 also heavily nudge you in doing things their way and come with a non-trivial size overhead (e.g. it is complete overkill to use Unity for your next Tetris clone).
And let's be honest, if you sit beginners in front of Unity they don't learn programming, instead they learn "Unity problem solving", e.g. "Unity trivia" which is hardly applicable to other contexts.
In my opinion, Unity is the Photoshop for game creation, you work on a very high level, but it's also very convenient (if you actually follow the rules and workflows).
But there are quite a few commercial games which use Unity only as a 'cross-platform wrapper', because their game client is more or less just a dumb input+rendering client, and the actual gameplay stuff all happens server-side.
It would be awfully nice if Unity could be split into a couple of standalone products (however that probably won't happen because it doesn't make much commercial sense):
- a low-level platform-abstraction library which contains all the driver-bug workarounds and behind-the-scene-fixes that have been accumulated over the years
- a 'bring-your-own-engine' asset pipeline and editor
- and finally, the actual Unity runtime engine, split into modules