I think part of the rationale here is that when you allow the bottom nav to enter the system back stack, things can get overloaded and confusing pretty quickly. In theory the app could put every single tap of a destination into the back stack, which makes a really really long trail to follow. Or it could cut off after some point, but deciding what that point is and how it’s reached can result in behavior that’s unclear to the user.
It could probably also be argued that how you present the destinations and their content plays a role — the bottom bar is a persistent component, and using the transition shown in the Material spec implies that you’re dealing with a persistent canvas too, placing you on one canvas at the very top of the app.
