Homebrew has had to deal with this in its sometimes-painful transition over the years from being a build-from-source system to a binary package manager. Suddenly you can't just have some package require the boost package be built using the --with-python flag, you either need to have it on in the bottled version (but wait, then boost has a dependency on Python, is that okay?), or you have to ship a separate boost-python, like Debian (but wait, then it's no longer a 1:1 mapping of recipes to bottles, is that okay?).