The restore deliberately uses the backup folder name so as to not overwrite the original files. This is a safety mechanism to ensure that a mistake is not made when restoring (oops my original files were ok I didn't really want to ovewrite them)
There is no Save As in Moneydance, the file structure is not a single file it is a complete folder tree that can contain many files including attachments, so a Save as function would really have to be a delete and rename function to overwrite an existing folder or a rename function if the other folder did not exist. Again it could be a little dangerous it it was that easy to do and Moneydance likes to err on the safety side, not unreasonable when you are taking about your financial history.
So the process where you use Operating system level tools like Explorer is the approach to take. I think it is something that the developers want you to be taking explicit action to do hence not adding a menu item in Moneydance to do it.