Does Unreal Engine currently support making plugins that add to the packaging process (e.g. adding options to the Project - Packaging menu, performing extra steps during the cook process, modifying the packaging output) or does one have to modify the code for the parts currently responsible for these directly?
No, there is not, main reason is code just need to be build, content need to be in uncooked form and your plug in need to be cooked in to the game when it’s packaged. Wait a little when Plugins gonna apper in marketplace so see how they should be packaged, or ask somebody reponcible for marketplace content validation that you interested in packageing the plugin for marketplace and how you should prepare it.