All my apologies, my first answer was wrong!
The perSpeciesCoverage.txt is doing what I described.
The fractionMissing.txt is counting the number of gene copies (so after a duplication, a gene will be counted twice) for a given species over all gene families. This number is divided by the the number of gene copies for the species with the highest number of gene copies. And it's then outputting one minus this ratio. So in the end, the species with the highest number of gene copies will have the value 0.
I don't remember why I output this file, I can't think about a good usecase for this weird quantity...
Does it make more sense with your data?
Best,
Benoit