So far as I can tell your post is actually "casually wrong". The sunflower seed example given by Chomsky seems to be mathematically well supported as a representation of Phi/Fibonacci sequences [1][2]. There's no mystification going on here, Chomsky is simply saying we don't fully understand the morphogenetic systems that produce these results. You offered some speculation as to why this might be, but so far no formalized results. Rene Thom did some excellent early work in this area, and demonstrated that chaotic dynamics can help to model some of these issues, but the topic is far from fully explored [3].

[1]: http://www.popmath.org.uk/rpamaths/rpampages/sunflower.html

[2]: http://www.maths.surrey.ac.uk/hosted-sites/R.Knott/Fibonacci...

[3]: http://www.amazon.com/Structural-Stability-Morphogenesis-Adv...