I'll second this question/request.
But I have to qualify it with wondering if the desired functionality has been there all along and I just don't know how to use it. Recently, I've been looking at the Save As Template option in the save dialog for the Ship Designer. There's no screentip for it, no info in the wiki yet, and I've not hunted the forums hard enough to find any explanation there.
Having the 'Update design to latest version' button be useful might be as simple as saving a custom base design as a template and then picking using the Use Design command on it when you're ready to build a better model?
Another case of me thinking about stuff but not having enough time to test or really dig into the forums...