Pulling the debian builds and modifying it to instead of Boost use the MNMLSTC headers does not result in a package being built with the bundled headers. 

The issue is in the use of 

cd build && make -j1 install DESTDIR=/wheremysourcepackageis/debian/tmp AM_UPDATE_INFO_DIR=no

At the dh_auto_install part - for some reason the EP_mnmlstc_core target still operates with the original install directory running into /usr/include/bsoncxx. You can see the 
fix-includes step operating on the locally installed files and not the ones under debian/tmp
 
My reading hasn't given me anything useful on how to translate the DESTDIR across to the ExternalProject part. 
 
This might be by design, but it would be good to have this as part of the install if using MNMLSTC - we have a Boost conflict in our case and would like to use something self contained for Mongo.