Ed,
     A week or so ago I included a statement by my son at age five that may be of some relevance here:  I wish I was a fairy so I could put a spell on you and you would live forever.  It includes subordination that is fairly routine at this age:  the content clause I was a fairy and adverbial subordination of the so that variety.  Relative clauses (especially nonrestrictive) may indeed come at a later date, but certainly adverbial subordinate clauses and many types of content clauses are in the repertoire by age five.  You seem to be in danger of doing what you are warning others not to -- lumping all subordinate clauses together. I think we also need to be careful about assuming that all these structures appear in our writing as transformations.  If they do, they shouldn't be thought of as stylistic.  Complex clause structures seem natural to speech.  What writing tends to lead us toward is complexity built into noun phrases, a response to the pressure to build considerable meaning into the clause itself.  Relative clauses and appositional phrases may indeed be responses to that pressure, since both are involved in postnominal modification.  Other kinds of subordination are much, much closer to speech.
     Language acquisition is not my area of expertise, but your cautions seem worth serious consideration.  Like you, I am appalled at the lack of knowledge students bring to college.  It's not just lack of knowledge, but terrible misinformation and misunderstanding, some of which I'll pass on when I have the time.  I don't do it often, but I sometimes debrief my students on what they know before teaching anything, and the results would be comical if they weren't of such serious consequence.
     I don't think you can teach clauses without teaching phrases.  I note that you start your own KISS grammar with prepositional phrases.  I would like to argue for constituency as a fundamental early concept, with phrase and clause as the core of that.   Wouldn't it be wonderful if students came to college with that?

     Craig