OK, I have a solution. It should now work that you can specify a target-os condition when configuring the python interpreter. The init for python.jam always had optional conditions for the interpreter, but unfortunately it was not usable for target-os because of the way it added the global toolset requirements. I've fixed that now. And I've also changed the Boost status/Jamfile to only use the host-os python interpreter accordingly. In your case all you need to do is add <target-os>??? when doing the "using python ..". That's assuming you build with "target-os=???". You might have to add a plain "using python ;" to configure the host-os python interpreter also, which is what the library check tests will use.