The vast majority of Stone’s program I’ve seen are done for %'s of set-rep maxes. That is, the %'s are from the maximum of whatever sets and reps you are doing and NOT from a 1rm.
I have only seen two of his programs that used a 1rm. One from 2007 and one from the early 90’s and they were used for athletes who had only known at that time 1rm’s and not what their set-rep bests were. The one from the early 90’s was used in a presentation on programming he gave and the one from 2007 was for incoming freshmen at ETSU who had little experience using a set-rep best (maximum for sets and reps) system.
So, if someone is doing working at a moderate load (for him this means 80-85%) for 3 x 10 or 3 x 5 or 3 x 3 that means the percentage is 80-85% of the most weight that individual can lift for that specific exercise for 3 x 10 or the other examples and not a percentage of their 1rm.