Replaced SSD drive on MBPr shown as External
Yes, having had the same issue myself you need to erase and setup the drive again from scratch. It comes from the factory setup as you describe for whatever reason.
After backing up all your data (or if you already have a good backup or don't need one), follow these instructions:

Power off your Mac. Power on then immediately hold the Left Command, Option and R keys

This will Boot to Internet Recovery Mode on your Mac.

Once booted, go to Utilities, Terminal.

Inside Terminal type the following:

diskutil unmountdisk disk0

gpt destroy /dev/disk0

Close Terminal.

Open Disk Utility.

Click your OWC Aura drive on the left side, then choose the Erase Button.
Once erased, close disk utility and then choose Reinstall OS X and choose the newly reformatted volume.

You should note it appears as a regular internal drive now.