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That game description seriously needs an update, as Ryo or Maria you're transported into the D-Movie that Sayaka is within who wanted to escape her troubling life (that in question is about her mother not letting her go with her boyfriend alongside other issues) and you're technically fighting inner demons of the girl as it implies her subconsciousness is merging with the D-Movie.
It goes deeper than that as what I described as I could only get this info from unfortunately; machine translating the game manual back in 2023. There's more information of the game's story in said manual.

Apparently, the unused theme is used, but under the strangest circumstance to encounter it. First, you must be at Track 2 (the level that takes place in the Shinjuku Underground Mall) Second, you must be already at the part where the subway trains show up. Third, you have to get killed by the enemies encountered there. Fourth, once you're dead and on the "Retry or Quit" screen, select "Retry", you're brought back to the subway train station area and now the supposed "unused" theme plays in said area.
I got this info from The Cutting Room Floor's talk page for this game.

ngl the final boss theme sounding closely similar to Ave Maria is genius, actually.