The narrative problem with the kids arriving in Federation territory in a stolen ship was that the Protostar would be impounded and the kids would be sent packing.

They needed a narrative reason to give the kids a chance to command the Protostar and have their own adventures, which means dragging out returning it to Starfleet. But rather than resorting to stalling tactics, they opted to have the kids fight to keep it out of their hands, and for good reason.

With Picard and Discovery, I felt more like that trope was used because the writers had no better ideas on how to keep the stakes high.

With Prodigy, I felt that the stakes were made essential to its premise.