Can you elaborate on what you mean by that and how building from source is different?
I presumed (perhaps wrongly) that you were planning to add the pip/setuptools installed packages to your backup, which would use a lot of ram and make booting slower. You could however make personal extensions out of the packages (as long as you could figure out which files were needed).
Another problem with pip/setuptools installed packages is that they always seem to use *egg files, which usually contain unneeded bloat. If you compile from source, it often does not result in *egg files (as is the case with olefile) or, can be prevented with "--old-and-unmanageable". This being said, with pillow, I had to manually unzip the *egg file to strip the libs and remove bloat.