Grant Cohn has a narrative and is not really a reliable source within the 49ers locker room. He pissed off several players within the last two years.
The more logical explanation is that Trey has had some unfortunate injuries that have stunted his growth. Purdy came in and played very well while showing an ability to read and react quickly to NFL defenses. Shanahan still sees Trey’s potential, but needs Trey to take the “next step.” Meanwhile, Purdy has earned starter reps based on his play last year.