I will suggest you to use latest rtPanel. You can download if from here.
We have already uploaded latest version on WordPress repo. You can check status here.
About parent theme changes:
If you are using rtPanel theme as parent theme itself then I will recommend you to do not make changes in parent theme directly, Since you lost your changes after updates.
If you will rename rtPanel theme to your theme then you can make changes in it and use your own child themes. But your will not able to get future updates of rtPanel.
About PR on github:
Yes you can create issues related to rtPanel.
I can not reproduce your mentioned issue. Please try again after update Sass and Compass.
About empty style.css
Actually it depends on developer. If you want to modified some styles of parent theme you can simply add you styles here. If you want to make lot of changes like layout, colors and other settings provided by foundation then you can simply enable full css and update Sass variables.
Let me know for further assistance.