The places of sites in filesystem have nothing to do with dns. You can not point something to a folder in a dns record, so I guess you mix there something up. DNS records point to an IP address. I'am pretty sure that the website setup is working properly as I tested it yesterday in RC2.
When I add another client and website it points to the same index file and I don't seem able to change it.
I'am sure that it does not point to the same file. The file might look similar as every new site gets a default file but it is not the same.