Using system codecs comes with its own set of problems, like making sure handling of encoder/decoder delay stays consistent.

On other system (Windows), we thus have already removed support for system codecs using MediaFoundation by now in libopenmpt because of this reason.
Staying with the most feature-complete default libraries (libvorbisfile and libmpg123) and providing a single maintained fallback library (stb_vorbis and minimp3) is the way we will continue to go. Maintaining system-specific codecs is too much maintenance overhead.