I never actually played 4 swords (what with it requiring 3 other people to play), but in Sappy at least, it plays back significantly crisper.
The main notable thing is that it has half the normal number of ticks per measure (96 as opposed to the midi standard 192).
This is why the tempo value gets halved, and why modulation values need to be halved when porting down from DS or up from GB, because both of those systems work on a 192 tick measure system.
The M4AA engine is very bad at modulation at high speeds (see the utter failure of it to correctly play back the GSC Rocket Hideout as an example).
Finally, it doesn't seem to have any obvious way to control the noise channels, unlike the GB, although it may simply be a case of finding the right conversions, and the engine has nothing to do with it.