With the MIPS instruction cache, this means that two consecutive SNES CPU instructions using e.g. the same addressing style or the same opcode have a chance that the second one will use the first one's code and that it will be cached.
In addition to having less sound skipping going on, certain platformer games (I'm looking at you, Super Mario World) are helped by having more synchronised controls. In other words, synchronising the audio also synchronises the controls a bit more.