I don't know if you watched it, but I don't think he says it was a staple workout or that it was run frequently, just that it's the famous one they ran. He doesn't say his kids do it often either. He mentions his kids don't do it until track season, and even then, it sounds like it's just a couple times per season. He talks about Nico starting out with 1 mile and progressing to over 4, which sounds like something that would take place over more than a year.
His exact words are "My top guys do the classic Prefontaine workout, the 30/40 workout," and, "That 30/40 workout is an example of a workout you might throw in there, here or there, where I work on that they're able to [hit those paces] by the end of the season, or [a workout] like that." Both of those make it sound like it's something he only does a few times a year, and nothing points to the idea that it was a staple workout for Oregon, it's just a famous workout.