Refactor custom timeouts support to match TF

[t0yv0]

Logging a design conversation from reviewing #2407

There are now good tests to cover Custom Timeout support. But there is one concern introduced in 2407. Currently timeouts are read through the InstanceDiff object from the planning phase and re-injected in PlannedPrivate.

This must not be how TF CLI operates itself, since the TF CLI cannot observe the InstanceDiff object and instead operates primarily via the TF gRPC protocol.

Likewise, PF resources and "any provider" support operates purely off gRPC protocol and must implement timeouts in a different way.

This task is a reminder to factor custom timeouts support to match how TF does it without relying on the InstanceDiff object, and to confirm it works for the PF case as well.