In addition to the Window > Preferences > General > Workspace setting for new files that you already know about, there is a File > Convert Line Delimiters To option. I don’t know of any existing plugin/tool that will do this automatically when you save, but you could certainly write one or make converting the line ending part of your process.
To make it easier on yourself, you can bind keyboard shortcuts to the conversion commands by going to Window > Preferences > General > Keys and filtering using “delimiter”:
