Remove logged errors for feature flags not implemented in native when skipNativeAPI is used (#49050)

Summary:
Pull Request resolved: https://github.com/facebook/react-native/pull/49050

Changelog: [internal]

We added support for feature flags that don't have a native module definition so we could handle cases where the JS changes progressed faster than native ones, but we recently saw that when native catches up, the API starts logging an error through `console.error` about the native module method not being available.

That's an expected result of this feature and it's when we can clean up the code in JS, so we shouldn't be logging errors in that case.

This removes the error for them specifically.

Reviewed By: elicwhite

Differential Revision: D68843247

fbshipit-source-id: 730f3eba8c26959825cd9c3897f055a02a5f9591