Midi is a constrained way to specify sound/music. My reading from wikipedia shows that microtones aren't a fundamental part of Midi, but are an optional additional standard which SoundNote doesn't seem to implement. My understanding is that it's using some common Java library for this purpose. See this for an example of someone asking something similar about microtones. There are other limitations in Midi such as a max of 15 simultaneous instruments for example.

I should also note that Midi and waveform specifications for sound are analogous to vector graphics and raster graphics respectively. They can be difficult to mix. Just as it is difficult to turn a raster graphic into a vector graphic, so too it is difficult to turn a waveform into a midi file. However, while converting from a vector graphic to a raster graphic is pretty easy, going from Midi to a waveform is hard. You basically have to export the midi file and then open in a program that can convert it into a waveform like format. This fact might be important to you as you try to work around the limitations of common implementations of midi.