Specifically, it describes a practice already in use, known as modal rhythm, which used the rhythmic modes. In this system, notes on the page are assigned to groups of long and short values based on their context. De mensurabili musica describes six rhythmic modes, corresponding to poetic feet: long-short (trochee), short-long (iamb), long-short-short (dactyl), short-short-long (anapest), long-long (spondee), and short-short (pyrrhic). Notation had not yet evolved to the point where the appearance of each note gave its duration; that had still to be understood from the position of a note in a phrase, which of the six rhythmic modes was being employed, and a number of other factors.Modal rhythm is the defining rhythmic characteristic of the music of the Notre Dame school, giving it an utterly distinct sound, one which was to prevail throughout the thirteenth century.[New World Encyclopedia]
Did a bookshop opener write this work? Evidence suggests that it was written in 1240, before John was born (he lived until 1320, so writing in 1240 was not possible), but his name is attached to it, leading to the assumption that he edited the work, or at least wrote later chapters of it. Some of the records of the time refer to John as magister, however, suggesting that he was a teacher at the University of Paris and not just a seller of books. How much he had to do with this work is unknown, but the connection made to it historically is accepted in the absence of other evidence.
For more on the history of musical notation, see here and here.
For information on bookshops in the Middle Ages, well, you'll just have to come back tomorrow.