There should be --public-headers-dir1 (and --public-header-dir2) option to abidiff to tell the tool where to find the public headers of the libraries to compare. By knowing where the public headers are, the tool should be able to auto-generate (and use) a suppression specification that suppresses reports about changes touching types functions and variables that are *not* defined in the header files found under the directories specified by --public-headers-dir1 and --public-headers-dir2.
It looks like the final option names are going to be --headers-dir1 and --header-dir2. Stay tuned.
This enhancement request has been addressed by commit https://sourceware.org/git/?p=libabigail.git;a=commit;h=e19bf5627a6a2720e6f762266d5b993305af4258 in the master branch of the Git repository. With this commit, specifying the public headers directories of the libraries being comparted with abidiff, using the --hd1 and --hd2 options, makes the tool automatically filter out changes to types that are not defined in said public headers. This should be available in the 1.0.rc5 release.