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The native API provided by the platform is not part of the W3C or Fido specificaitons.
That is defined by the platform vendors themselves.
Thre are currently two public ones.
Android (Yes it is missing CTAP2 functionality for extenal keys currently)
This uses digital asset links to share RPID between apps and
webRP.
The documentaiion will do a better job than I can explaining it. https://developers.google.com/identity/fido/android/native-apps
Your next question will be how do 3rd party browsers like FireFox work. There is a whitelist of browsers that google maintains that allows some special trusted browser apps to specify arbitrary RPID. This is the case with FireFox however Mozzilla broke the Webauthn code on Android independently in switching some of there underlying code and it reamins broken to my knoledge.
Windows 10,
All the browsers (including Chrome) use webAtuhn.dll, this gives them acess to both the platform and roaming authenticators.
App signing on windows is not all that it could be, so win32 apps names are displayed in the dialog, but I don't beleve at the moment that anything is used to validate the RPID.
Apple currently has an non native API approach
Native apps are expected to do authentication in a
SFSafariViewController or ASWebAuthenticationSession and those use
the RPID of the web page loaded.
I would expect when/if Apple releases an API it will be more like Android.
The native API are to the frustration of some outside the standards process.
Regards
John B.