Whichever python you use to do run the initial bootstrap.py is the one that will be used for your entire project. All paths will reference that specific python and the sitepackages for that specific python will be used.
This is one of the best things about buildout
This is a 32 bit python 2.6:
/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 boostrap.py
This is a 64 bit python 2.7:
/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python bootstrap.py
Now go look at the bin/ it created.
Then do your actual bin/buildout -c dev.cfg and look at the scripts in the bin. For my 32 bit example:
For the first one I see in my django file:
#!/Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python
...
'/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages',
The accepted answer says you need to compile a whole python. This is not needed nor advised, though it would mean you have a completely isolated sitepackages. But there are easier ways to tell buildout to not include the sitepackages.
The answer from esaelPsnoroMoN is actually correct, but s/he didn't describe the solution very well. (I ignored it myself before)