The SCDS loader, while based off of Moonshell, is still highly customized for the SCDS hardware (for instance, the ability to launch commercial games, patch files on launch, etc.) so a simple rename won't work. You're stuck with 1.41 there.
Also, if you want to try it out (and I can't believe I forgot about this earlier), SNEmulDS has an "SPC Jukebox" feature that lets you play any SPC file instead of whatever the game is playing, so there's another DLDI-capable SPC player you can try to see if you like it. It won't be as easy to use as Moonshell, and all your SPC files will have to be in the "SNES" folder, but perhaps you might get better audio quality this way.
Granted, it'll probably sound exactly the same considering there is only one SPC engine out there which is used by Moonshell, DSOrganize, PocketSPC, and every SNES emulator for the DS, but it's still worth a shot.