if you are not already using it, use Packages to generate your packages based installer. It’s much easier than trying to work with the tools Apple provides. It has a command line interface, so you can integrate it in your build script. Availabe at http://s.sudre.free.fr/Software/Packages/about.html
IIRC you need a flat package hierarchy such that your installer will work in El Capitan. I have one package for each plugin format. This enables the user to specify the plugin formats he wants to install.
Bonus tip: Add a pre-install script to each package to uninstall a previous plugin version from the system. Why? Because if you just replace the old plugin, the creation date wont change (only the modification date). Some hosts (including Pro Tools) only trigger a rescan of your plugin if the creation date got changed. Also do this in your Windows installer.