Following some investigation at en:Category talk:Pages using deprecated score attributes, it seems that adding override_audio= or override_midi= will cause the containing page to be added to Category:Pages using deprecated score attributes. Why? Can that behaviour be stopped?
Topic on Extension talk:Score/Flow
This was mentioned in Project:Tech News/2019#Tech News: 2019-25
The TimedMediaHandler extension now handles MIDI files, so that putting a wikilink like [[File:somefile.mid]] creates a player. Eventually (phab:T135597) Extension:Score will lose its redundant code, hence the deprecation. I added an explanation of why these attributes are deprecated to this page and how to fix. I haven't added this yet to en:Help:Score.
The behavior won't be exactly the same (e.g. the better MIDI file won't be shown when you click on the score). I wonder why pages override the generated MIDI and audio; their generation has improved.
The generation of MIDI files may have improved, but I think the override is mostly done with .ogg files. These could be sound files from actual performances, or from MIDI files that editors have created in their own environment with Soundfonts or similar which most likely generates better sound than this extension. Then there are cases where LilyPond doesn't produce certain ornaments at all.
The non-deprecated override method mentioned overleaf, "Deprecated, instead you can add a [[File:name.oga]] wikilink after the score tag." doesn't seem to work; see en:Help talk:Score#Obsolete and deprecated score attributes, including override_midi, override_audio, override_ogg.
Sorry, I should have said "after the closing </source> tag." I also responded on that en-wiki talk page.