“With regard to audio file formats, are there advantages to AIFF over SDII or vice versa?”
These are both uncompressed file formats, which means no data is thrown away in their making. Therefore they should, under all normal circumstances, sound the same. You should use whichever format is most compatible with the equipment you are using. Of the two AIFF is in more widespread use, but Sound Designer II (SDII) files tend to be used more in pro DAW systems. Many devices can read and write both of these equally well.
When you get into compressed file formats, like MP3 for example, the rules drastically change. Quality differences among them can vary widely, and can even differ quite a bit within any one type depending upon the algorithm used to generate the file from the uncompressed data.