If some are to be considered private then the questions are: which ones and how to fix. Presumably renaming to start with "_" might break existing code, so maybe adding an __all__, and just including the public objects is better? That could break code existing relying on * imports I suppose. Deprecation is another possibility, although feels a little odd for things never documented.

formatannotation and formatannotationrelativeto look like a helper functions for formatargspec and are probably not intended as part of the public interface.

Similarly walktree looks like a helper for getclasstree (and its docstring describes it as such).