I'm not sure if this is an intended behavior, but adding an annotation to a page produces a new page version which affects the programming rights status of a page. Adding a comment creates a minor edit, which does not produce the same result (should it?), but the new version an annotation creates seems to initiate this effect.
Given this, it's not possible to have a page be enabled with Programming Rights, while also opening it up to commenting / annotations. Perhaps this is by design, as comments and annotations are potential entry points for injecting malicious code.