Eh. If I get motivated enough, I might try to figure out more about that engine. Yeah...kinda sounds like a pipe dream for me! {XD} Who knows, though? I might step up in hacking skill someday.
And I definitely wouldn't say the samples are low quality. Those are pulled straight from the original game! They sound clear as crystal when played back in Sappy. To be honest, I think it's just the standard sound quality disparity between the GBA (when playing a decently-demanding game) and other systems that sample sounds. I wouldn't say I'm an audiophile, but things like this are just really jarring to me.
The only SNES -> GBA game conversion I can think of that used the same, unaltered music from the original is The Legend of Zelda: A Link to the Past. I noticed that the sound in that game had a noticeable clarity drop, too (at least when played in VBA-M), so it's probably just to be expected.