I'm going to guess that as soon as you pop that drive out of the enclosure, the warranty is done.
I accidentally bought a 2TB external drive... ran it for a bit. It seemed to run quite hot so I just pulled it out of the enclosure and mounted it internally... where it ran much cooler... with the understanding that the warranty was rendered moot at that point. I lucked out, the enclosure contained a straight-up Seagate Barracuda (7200rpm) drive, but I'll bet WD uses Greens.
I haven't looked at them in a while, but I recall portable drives had less warranty than their internal counterparts... but they have butchered most internal drive warranties down, anyway, so they may be the same now.
So I really just need a bare 4tb drive. My assumption is that a My Book external drive has a standard WD hard drive, why would they create a whole new product just to put inside an external enclosure? If I reformat it shouldn't it be just like any other WD HD?
Should be... however, you spend the money on an external... pop it open and find it's not correct or what you want... and you are stuck with it in any event because you voided the warranty by opening the enclosure. Chances are, with full size external (3.5") drives, you are getting a standard SATA interface drive.