Technically, there's no such thing as a factory AT 1391401 - the 1391401 implies the PS/2 cable, and 1390131 is the AT version.
Anyway, the 1391401 definitely counts. The 42H1292 and other successors just weren't QUITE as good, and while I've not typed on a Customizer, I'm liking my EnduraPro less and less, and liking my 1391401 more and more.
I don't know that the HHKB will count. See, the 1391401 had the advantage that it was widely spread. For several years, almost every new IBM PC came with one. That's a
lot of keyboards. Even today, you can get some used for $5 or so at the thrift store.
The HHKB is a niche market keyboard that only geeks buy. A few will remember it 20 years from now, but chances are, it won't be well known. In fact, I don't know that there ever will be another widespread cult classic keyboard like the 1391401 is now - the best current production keyboards don't have near the penetration of the other widespread cult-classic keyboards, the Northgate OmniKey and the Apple Extended Keyboard (including 2.) I shudder to think what will be out in 20 years... maybe the Dell QuietKey will be a cult classic, because it'll have better build quality and typing feel than everything else?