See [THE LAWS OF PESACH BY RAV DAVID BROFSKY](http://etzion.org.il/vbm/english/archive/moadim70/02-70moed.htm) from etzion.org.il
 
First part of the quote is background.

> Shiur #2: The laws of Pesach. Defining chametz. Two passages in the
> third chapter of pesachim discuss the definition of “chimutz”
> (leavening). one passage (pesachim 48b) presents the physical
> characteristics of chametz. the mishna describes the leavening process
> as follows: first, the dough becomes pale, similar to the appearance
> of a man whose hair stands on end out of fright.  next, cracks begin
> to develop on the dough’s surface, described by the mishna as “karnei
> chagavim” (locusts’ antennae).  the cracks then begin to increase and
> merge into each other. 

This part of the quote is the main point:

> The Rishonim and the Shulchan Arukh (451:2) rule in accordance with
> the Sages (and R.  Meir) regarding the definition of chimutz. it is
> forbidden and punishable by karet to eat the mixture once it has
> developed cracks like a “locust’s antennae.”
> 
> 
> R. Yosef Karo, in the Shulchan Arukh (459:2), concludes:   One should
> not leave dough without it being worked, even for a moment.  **as long as one is
> working the dough, even for the entire day, it does not become
> chametz.**  If one left the dough without working it for a mil, then
> it becomes chametz.  the period of a mil is 18 minutes.

From this we see that the halachic status of chimutz is specifically related to the appearance of the dough and not to some chemical status. The [chemical fermentation process](http://www.britannica.com/EBchecked/topic/334116/leavening-agent) of leavening will continue  while the dough is being worked.

So yes,  the concept of chametz is to be treated as a purely halachik construct independent of the "physical" (I prefer to call it "chemical") phenomenon of yeast/gluten interaction.