As I understand it, the S3 HD, the S3 HD XL, and the S4 TiVos expect a particular Western Digital drive model number. That's the number the drive itself reports back when its firmware is properly queried, not anything the enclosure has to say.
So you have to use that particular model WD 500GB or that particular model WD 1TB drive, connected to the TiVo's eSATA port, regardless of whether you have it inside an enclosure or just lying out there in the open.
If you have not yet married an external to your TiVo, you might want to consider using jmfs to create a larger internal and put the original on the shelf for safe-keeping rather than risk the extra chances of one of two drives failing and taking out all of the shows recorded since the connection of an external.