so you mean that these instructions being very in depth about desire and what not and the zen idea of, as Dan74 put it, "what arises, arises" are different in this way?
I'm not really sure, as I have not practiced either Theravada or Zen formally with a teacher or sangha. But what I've noticed over the years (from talking with people in both groups) is that for those practicing Theravada the path seems very clear. Buddha laid out the instructions, you follow the instructions, find others (sangha and/or teacher) to support, guide and encourage you, and positive results unfold gradually over time.
With Zen the path seems less clear. Most Zen Buddhists believe a teacher is needed, that much about the path and practice cannot be communicated with words and descriptions, you need to be in close proximity of someone who has mastered Zen. But then some discover this doesn't work, in practice, all the time. The Western Zen community is going thru a bit of a "crisis" right now, with revelations of sexual misconduct by a number of respected Zen teachers.
How could this happen? I think its in part this belief that the path is not easily described, putting too much faith in teachers. Also a lack of emphasis on ethics and moral conduct (sīla), especially in Japanese Zen. Which I think is initially seen as something positive by many drawn to Zen, but then eventually leads to these incidents.
But I'm not sure. It's just something I've observed from a distance, and a problem I've wrestled with as well. Dan probably has a better understanding of this as he has been fortunate to have a Zen teacher who does emphasize sīla. For Zen teachers who have truly mastered the Dharma and recognize how essential each component is they probably provide assistance (and have an understanding of the path) that is closer to what Theravada provides.
Again, just my perspective.