I completely get that. In fact, it makes sense to me considering that this "GB Player" routine is, essentially, just a more widespread version of the single tune switching routine seen in Shiny Gold. It does seem more useful than single tune switching, though, considering that the games today probably use completely different playlists for day/night tracks (or the poor man's GB Player/Sounds item in HG/SS).
(If I just angered any DS music hackers out there because of my incorrect notions, I'm sorry. I do intend to check out hacking for games on the system sometime soon.)
EDIT: I just took a look at your code, and it does seem quite helpful for its stated effect. Of course, it won't help for those one-off situations that you mentioned, especially for scripted Wild Pokémon battles. In that case, it would only negatively affect legendary scripted battles, as standard scripted battles work fine with the "dowildbattle" command. Could a similar routine change which Pokémon get attributed to the legendary music instead of the R/S/E trainer battle music?
If this question is getting too off-topic, feel free to PM me.
The song group appears on the assembly page, in case you were confused about that.