You can find SATA RAID controller cards with external SATA ports, so it's not really an issue. You do not use onboard controllers with anything but very low-end servers. Try to find one without a RAID card, and then you can add your own SATA RAID controller with external ports.
To start you off on your search, look at the HP ProLiant ML series of pedestal servers, or the DL100 series for affordable rackmounts, and add a 3ware RAID controller with external ports. I know they make one, as I have seen one recently.
Or, you could just use one of these brackets with any onboard SATA ports: