"Miracle plays" probably refers to the form of theatre known as a Miracle play, the medieval plays concerning biblical or biblically inspired stories. I suspect that Schwartz's original idea was to follow on from his Godspell success with a sort of - and this is where it gets complicated - Morality play, with Pippin a sort of Everyman passing through the journey and temptations of life.
Morality plays were not the same as Miracle Plays ... but both were a form of medieval theatre, which pertains, somewhat, to the era of Charlemagne only about three hundred years before.
So I suspect that the phrase "miracle plays" stems from this apparently garbled theatre history. Not that Schwartz was garbled - he may have had a very specific usage in mind regarding his plan for Pippin. But Fosse changed it. I donlt know all the intricacies of how he changed it, but it has been said often enough that the expression of Schwartz's ideas was changed.