The drive within the 3TB My Book is indeed a 4KB-sectored Advanced Format drive. However, it still reports to the outside world that it has 512-byte LBAs (logical sectors). WD refers to this as "512-byte emulation (512e)".
Between the drive and the USB port is a USB-SATA bridge chip. This chip enables the drive to communicate over a foreign interface. Simply put, the PC speaks USB, the drive talks SATA, and the bridge IC is their translator.
In the case of the My Book, the bridge also fakes the drive's logical sector size. That is, the bridge reports to the OS that the external mass storage device has 4KB LBAs. Therefore, when the OS writes a 4KB LBA to the drive, the bridge breaks it up into 8 x 512e LBAs, and then writes them to the drive. The drive then takes those 8 LBAs and reassembles them into a single 4KB physical sector. At least that's how I understand it.
If you follow Joe's link, the author writes that the Partition Size Limitation is 4,294,967,295 sectors. This number corresponds to the largest number that can be represented with 4 bytes (= 0xFF FF FF FF). Traditionally, the sector size is 512 bytes, so the total capacity works out to be 2TiB.
However, in the case of the 3TB My Book, the sector size is 4096, so the maximum partition size for an MBR partition is ...
4,294,967,295 x 4096 = 16TiB