Key point to note regarding PEP 432: at least personally, I'm not actually aiming to deprecate the legacy embedding API.

Instead, I'm just aiming to eventually stop *adding* to it, with new config structs replacing the current ad hoc mix of pre-init function calls, C globals, environment variables, and filesystem state.

That means I'm quite willing to accept maintaining compatibility for applications using the current single phase initialisation approach as a design constraint for the PEP.

We have a similar constraint in place for extension modules: 
even though any *new* features we introduce are likely to be dependent on switching over to PEP 489's multi-phase initialisation APIs, we still ensure that single-phase initialisation continues working for existing modules.