Reporting a map without the noise of entries that are smaller than the threshold is the explicit purpose of the applyThreshold method (https://github.com/cyclus/cyclus/issues/483). It is not extracting anything. It is simply reporting a thresholded map. It is not better to leave tiny things in because that would defeat the purpose of the function. 

This was discussed somewhat in https://github.com/cyclus/cyclus/issues/484, but I'll repeat it here : the choice to use this function in certain ways may result in modeling inaccuracies. However, used correctly, the information provided by this function may also help the developer be more accurate and deliberate about modeling approximations.

The threshold function doesn't get rid of information in the compmap. It just returns a thresholded map for informational purposes. Specifically, it returns a map that results if you zero-out elements that are smaller than the threshold. That is it's purpose. For reasons why, please see the discussion cited above discussing the use cases that this addresses as well as my comments and @gonuke's responses to your previous questions on this order. 

tl;dr:
It is a modeling tool, mostly useful for saying "What would this compmap look like if we ignore things that are smaller than what I care about." So, it should do that.