The method a lot of Linux distributions uses is to have a non-free repository located in some jurisdiction without software patents and not too friendly to America. So after install, you add the non-free repository and install stuff like VLC.
It is also possible to compile a media player to not support various codecs, so with FFmpeg and I presume VLC, you could ship a cut down version that only plays patent free codecs. VP9 (and lower numbers) for video and Opus and such for audio. Things like MP3 where the patents have expired also could be included. Probably still not worth the hassle for Arca Noae, especially in America where it is so easy to get sued and even when in the right, too expensive to defend yourself, so we'll be left installing this stuff after the main install.