as far as variants go - the one I have done so far was several measures; and had an indicated place of origin - so I did it up as a seperate midi.
I noticed in one tune that the transcriber had indicated a variant by stem direction. I went with the notes that followed the stem direction of the main tune.
As with folk tunes - these midis can only be a guide - In the section on singing the tunes the author mentions that temp could vary widely between singers or occasions. Likewise the variations on a tune are sometimes due to the words of the particular verse.
My feeling is the midi's will be an asset and guide - but can't indicate EVERY variation - at least not without extensive additional notes - much of which would probably be guesswork at this remove.
(My opinion - but backed by what I have read about spirituals, gospel, folk, etc in various collectors books)