So if there's something always running .... isn't the same as having on always on server (with auto scaling of some sort)?
For an app with low usage, you start getting a price that can compete with Heroku.
I dont think it's that simple to replace one service with another. It requires a lot of very sensitive dealing with external customers. And one cannot (easily) use the typical "Google deprecation" on a Cloud service offering, either.
So it's complicated. But your impression is not too far from the inclination.
One would assume transition from AppEngine to Cloud Run would be directed by establishing a pricing differential that incentivises moving off AppEngine.