I'm not really sure what you're asking here. The jamf binary has, to my knowledge, always downloaded pkgs/mpkgs to the /Library/Application Support/JAMF/Downloads/ directory before installing them. It's been like this forever. It can't install them any other way but to download them first to the local machine.
As far as that breaking installs with configuration files, if you have files that need to be in the same directory as the pkg when the pkg is run, what you need to do is create a folder in a place like /private/tmp/ and drop all your files (pkg(s) and configuration files) into that folder, then take that folder into Composer to build a new package from that source. Add a postinstall script to the pkg that will install the actual package using something like /usr/sbin/installer -pkg /private/tmp/foldername/packagename.pkg -tgt / as the code to run. This will install the package after it drops it into that directory, along with the config files that should also be in that same folder.
Hope that makes sense. If you need more detailed instructions, post back. There are for sure some existing threads that talk about this method in more detail that can be linked here for you.
