I find this whole line of thinking to be unconvincing.  Centuries of 
thought have tried to convince people that one or another point of 
view is "Truth" and everything else is mere illusion.  The notion 
that there is some "Super" truth behind mere, everyday truth is a 
religious notion that serves no purpose whatever.  
Why should we think that holism is more real than boundaryism?  Maybe 
holism is an artificial construct of the mind.  It may, in fact, be 
impossible to think of anything at all without thinking of at least
two things that are some somehow related and interacting.  Try, I 
mean, really try, to think of just one thing without it being related 
to anything else at all.  What could you possibly be thinking of?
This discussion of mine is inadequate, to be sure.  My sense is that 
extropians and transhumanists shouldn't try to re-capture a religious 
sense in mystical notions of holism vs. boundaryism.  Let's just use 
the theories for what they're worth and forget about which one is 
more "true" than the other.
BTW, I have found Lee Smolin's "Life of the Cosmos" to be a most 
compelling discussion of these types issues.
Ciao,
think of