Sorry, I've never used the "config" command nor seen any code that does, nor any documentation for it.  I didn't even know it was actually usable.

The OP's rationale for the change sounds reasonable to me, but a quick skim of the module doesn't convince me that it'll fix the problem correctly, vs. e.g. using os.path.abspath().  One thing that bugs me is why the program's being created in the current directory instead of the build/ directory in the first place.  ISTM that there's a lot more that's broken here.   OTOH, I don't suppose the patch would make things any worse.  It would be nice if the original author of the module were around.