Very interresting posting.
You should read some books of the french philosopher Edgar Morin about "the complex thinking".
If I try to resume the part relative at your post (it's a little difficult for me to explain that in a language I don't really masterize, as you all noticed for my english) it will be :
1) As you notice very well : "The whole is more than the sum of his parts" for the reason you said. Morin define that exactly : "it exists emerging features, i.e. features appearing from the organisation of the whole, and who are able to retroact on his parts"
2) But he add : "The whole is too less than the sum of his parts" for the reason that "the parts can have features who are inhibited by the organization of the whole"
I let it in french here, if never I made a big mistake of translation and if a best english-speaking french-speaker is around :
1.« le tout est plus que la somme des parties » : « il existe des qualités émergentes, c'est-à-dire qui naissent de l'organisation d'un tout, et qui peuvent rétroagir sur les parties »
2. « le tout est également moins que la somme des parties » : « les parties peuvent avoir des qualités qui sont inhibées par l'organisation de l'ensemble »
The cover of the first part of the book "La méthode" where you can read the explanation of this concepts, really more great that what I can explain:
I don't know if it exists in english! I will check!