Builds in the OP updated with (untested) container persistence support.
The only missing part is FRED controls to enable it. However, you can add the persistence options in Notepad, which should go after the $Data line.
The options (case-insensitive, include the '+'):
+Save On Mission Progress
+Save On Mission Close
"+Eternal", if used, must come before the "Save On" option.
Even though FRED doesn't have controls yet, it should still load/save the container persistence options.
EDIT: Forgot to mention that persistent containers should work for "Red Alert" missions as well.