Part of the problem with understanding this sentence is its verbiage, the fluff of words that obscure what it says. When analyzing it, first look at its form by replacing several phrases by place-holders. Replace "The significance of culture and identity in development" with "Stuff", replace "the cultural factor in the process of development" with "stuff", and replace "abandoning Eurocentric development thinking" by "stuff", giving:
Stuff has to do not so much with stuff as with stuff.
If symbolically aware, you can instead write "X has to do not so much with Y as with Z". The notion that X has more to do with Z than with Y may now be more clear.
Regarding your other question, on why "has to do not so much" vs "has not so much to do", either form is usable; writers will use whichever they like. Possibly the author of the sentence treats "has to do" as a collocation, and never thinks of dropping anything into the middle of it. My opinion is that "has to do not so much" reads slightly better than does "has not so much to do". My opinion also is that the sentence cannot be expressed clearly without sounding silly because "culture and identity in development" and "cultural factor in the process of development" are nearly the same thing, while "abandoning Eurocentric development thinking" is a non-thing, an absence of something. The sentence is about as good as "X has more to do nothing than with X".