It seems they want to replace their managed AppEngine service through Cloud Run in the long run.
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.