`native-compile-prune-cache' does not remove the preloaded/ subdir (or its contents) of the native-lisp/ directories, and consequently does not remove the directories themselves.
For example, after running it I still have *.eln files in the following directories (comp-native-version-dir = "29.0.50-c0f9fe8e"):
~/.emacs.d/.eln-cache/29.0.50-c0f9fe8e
D:\Devel\emacs\repo\trunk\native-lisp\29.0.50-57ea32b2\preloaded
D:\Devel\emacs\repo\trunk\native-lisp\29.0.50-7c1dd663\preloaded
D:\Devel\emacs\repo\trunk\native-lisp\29.0.50-a22e1c10\preloaded
D:\Devel\emacs\repo\trunk\native-lisp\29.0.50-c0f9fe8e\preloaded
which means the command deleted the stale cache in ~/.emacs.d/, but not the ones in the source tree.
Is that intended?